SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/3_TTAGGC_L001_R1_001.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 8 bp from their 5' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc --threads 28 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.14 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/3_TTAGGC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 221.48 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 11,817,358 Reads with adapters: 4,606,953 (39.0%) Reads written (passing filters): 11,817,358 (100.0%) Total basepairs processed: 602,685,258 bp Quality-trimmed: 2,616,062 bp (0.4%) Total written (filtered): 589,618,988 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4606953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.2% C: 1.7% G: 21.0% T: 46.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3144638 2954339.5 0 3144638 2 749606 738584.9 0 749606 3 263293 184646.2 0 263293 4 117830 46161.6 0 117830 5 28890 11540.4 0 28890 6 25409 2885.1 0 25409 7 22726 721.3 0 22726 8 21766 180.3 0 21766 9 21567 45.1 0 21262 305 10 19726 11.3 1 18729 997 11 18046 2.8 1 17214 832 12 17149 0.7 1 16487 662 13 14709 0.2 1 14113 596 14 15359 0.2 1 14673 686 15 13107 0.2 1 12401 706 16 12953 0.2 1 12295 658 17 11724 0.2 1 11250 474 18 10539 0.2 1 10137 402 19 9528 0.2 1 9077 451 20 9185 0.2 1 8752 433 21 8416 0.2 1 7963 453 22 7405 0.2 1 7045 360 23 6672 0.2 1 6351 321 24 6253 0.2 1 5904 349 25 5200 0.2 1 4911 289 26 4304 0.2 1 4071 233 27 3663 0.2 1 3406 257 28 3422 0.2 1 3191 231 29 2902 0.2 1 2712 190 30 2295 0.2 1 2160 135 31 1760 0.2 1 1652 108 32 1385 0.2 1 1320 65 33 1043 0.2 1 995 48 34 669 0.2 1 641 28 35 389 0.2 1 368 21 36 250 0.2 1 229 21 37 108 0.2 1 101 7 38 87 0.2 1 79 8 39 65 0.2 1 59 6 40 52 0.2 1 49 3 41 64 0.2 1 64 42 127 0.2 1 125 2 43 180 0.2 1 169 11 44 330 0.2 1 313 17 45 541 0.2 1 525 16 46 591 0.2 1 568 23 47 434 0.2 1 382 52 48 87 0.2 1 83 4 49 36 0.2 1 30 6 50 40 0.2 1 33 7 51 433 0.2 1 349 84 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/3_TTAGGC_L001_R1_001.fastq.gz ============================================= 11817358 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 58516 (0.5%)