SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/1_ATCACG_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/1_ATCACG_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 168.39 s (18 us/read; 3.35 M reads/minute). === Summary === Total reads processed: 9,402,890 Reads with adapters: 3,614,450 (38.4%) Reads written (passing filters): 9,402,890 (100.0%) Total basepairs processed: 479,547,390 bp Quality-trimmed: 1,696,655 bp (0.4%) Total written (filtered): 470,451,893 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3614450 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 1.4% G: 20.7% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2534817 2350722.5 0 2534817 2 588836 587680.6 0 588836 3 204258 146920.2 0 204258 4 88103 36730.0 0 88103 5 17429 9182.5 0 17429 6 15373 2295.6 0 15373 7 13444 573.9 0 13444 8 12820 143.5 0 12820 9 12758 35.9 0 12524 234 10 11538 9.0 1 10942 596 11 10792 2.2 1 10254 538 12 10254 0.6 1 9851 403 13 8731 0.1 1 8342 389 14 9191 0.1 1 8738 453 15 8084 0.1 1 7583 501 16 7876 0.1 1 7481 395 17 6938 0.1 1 6639 299 18 6454 0.1 1 6171 283 19 5903 0.1 1 5610 293 20 5383 0.1 1 5103 280 21 5083 0.1 1 4790 293 22 4643 0.1 1 4397 246 23 4171 0.1 1 3933 238 24 3683 0.1 1 3464 219 25 3166 0.1 1 2987 179 26 2610 0.1 1 2451 159 27 2135 0.1 1 1984 151 28 1995 0.1 1 1857 138 29 1717 0.1 1 1614 103 30 1262 0.1 1 1188 74 31 987 0.1 1 907 80 32 773 0.1 1 723 50 33 587 0.1 1 556 31 34 338 0.1 1 315 23 35 167 0.1 1 159 8 36 102 0.1 1 95 7 37 53 0.1 1 50 3 38 53 0.1 1 51 2 39 33 0.1 1 31 2 40 32 0.1 1 28 4 41 41 0.1 1 37 4 42 100 0.1 1 90 10 43 111 0.1 1 107 4 44 262 0.1 1 252 10 45 411 0.1 1 399 12 46 385 0.1 1 361 24 47 255 0.1 1 228 27 48 45 0.1 1 42 3 49 27 0.1 1 20 7 50 17 0.1 1 16 1 51 224 0.1 1 183 41 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/1_ATCACG_L001_R1_001.fastq.gz ============================================= 9402890 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 37560 (0.4%)