SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/4_TGACCA_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/4_TGACCA_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 210.28 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 11,606,618 Reads with adapters: 4,470,755 (38.5%) Reads written (passing filters): 11,606,618 (100.0%) Total basepairs processed: 591,937,518 bp Quality-trimmed: 2,245,132 bp (0.4%) Total written (filtered): 580,602,143 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4470755 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 1.3% G: 20.3% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3147149 2901654.5 0 3147149 2 722625 725413.6 0 722625 3 250384 181353.4 0 250384 4 108481 45338.4 0 108481 5 21488 11334.6 0 21488 6 18853 2833.6 0 18853 7 16764 708.4 0 16764 8 16269 177.1 0 16269 9 15639 44.3 0 15347 292 10 14359 11.1 1 13593 766 11 13170 2.8 1 12541 629 12 12907 0.7 1 12430 477 13 10766 0.2 1 10328 438 14 11214 0.2 1 10771 443 15 9452 0.2 1 8948 504 16 9996 0.2 1 9523 473 17 8102 0.2 1 7741 361 18 7676 0.2 1 7357 319 19 7168 0.2 1 6807 361 20 6596 0.2 1 6255 341 21 5906 0.2 1 5567 339 22 5435 0.2 1 5122 313 23 4813 0.2 1 4560 253 24 4375 0.2 1 4118 257 25 3610 0.2 1 3432 178 26 2846 0.2 1 2668 178 27 2352 0.2 1 2171 181 28 2192 0.2 1 2045 147 29 1735 0.2 1 1628 107 30 1468 0.2 1 1364 104 31 1005 0.2 1 928 77 32 875 0.2 1 815 60 33 579 0.2 1 549 30 34 335 0.2 1 313 22 35 233 0.2 1 216 17 36 127 0.2 1 119 8 37 91 0.2 1 88 3 38 74 0.2 1 71 3 39 71 0.2 1 66 5 40 71 0.2 1 64 7 41 89 0.2 1 86 3 42 186 0.2 1 170 16 43 201 0.2 1 187 14 44 449 0.2 1 421 28 45 732 0.2 1 699 33 46 739 0.2 1 702 37 47 468 0.2 1 412 56 48 102 0.2 1 95 7 49 41 0.2 1 39 2 50 54 0.2 1 47 7 51 443 0.2 1 360 83 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/4_TGACCA_L001_R1_001.fastq.gz ============================================= 11606618 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 45960 (0.4%)