SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_15_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_15_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1315.43 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 68,857,992 Reads with adapters: 26,803,401 (38.9%) Reads written (passing filters): 68,857,992 (100.0%) Total basepairs processed: 3,459,545,810 bp Quality-trimmed: 4,066,729 bp (0.1%) Total written (filtered): 3,427,098,592 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26803401 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.8% G: 3.9% T: 38.4% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 25748064 17214498.0 0 25748064 2 670246 4303624.5 0 670246 3 304450 1075906.1 0 304450 4 62669 268976.5 0 62669 5 9679 67244.1 0 9679 6 889 16811.0 0 889 7 2500 4202.8 0 2500 8 1116 1050.7 0 1116 9 540 262.7 0 51 489 10 1303 65.7 1 15 1288 11 391 16.4 1 46 345 12 184 4.1 1 1 183 13 70 1.0 1 0 70 14 75 1.0 1 0 75 15 96 1.0 1 0 96 16 221 1.0 1 0 221 17 442 1.0 1 0 442 18 360 1.0 1 0 360 19 38 1.0 1 0 38 20 11 1.0 1 0 11 21 8 1.0 1 0 8 22 8 1.0 1 0 8 23 6 1.0 1 0 6 24 2 1.0 1 0 2 25 5 1.0 1 0 5 26 4 1.0 1 0 4 27 9 1.0 1 0 9 28 1 1.0 1 0 1 29 2 1.0 1 0 2 30 2 1.0 1 0 2 31 2 1.0 1 0 2 32 3 1.0 1 0 3 33 1 1.0 1 0 1 34 1 1.0 1 0 1 35 2 1.0 1 0 2 36 1 1.0 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_15_s456.fastq.gz ============================================= 68857992 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 873787 (1.3%)