SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/8_ACTTGA_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/8_ACTTGA_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 261.00 s (18 us/read; 3.30 M reads/minute). === Summary === Total reads processed: 14,374,642 Reads with adapters: 5,792,989 (40.3%) Reads written (passing filters): 14,374,642 (100.0%) Total basepairs processed: 733,106,742 bp Quality-trimmed: 2,401,819 bp (0.3%) Total written (filtered): 714,442,682 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5792989 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 2.3% G: 22.1% T: 45.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3740046 3593660.5 0 3740046 2 922606 898415.1 0 922606 3 342031 224603.8 0 342031 4 157961 56150.9 0 157961 5 48861 14037.7 0 48861 6 44020 3509.4 0 44020 7 40037 877.4 0 40037 8 38573 219.3 0 38573 9 38207 54.8 0 37685 522 10 35360 13.7 1 33447 1913 11 33552 3.4 1 31628 1924 12 32274 0.9 1 30595 1679 13 28017 0.2 1 26496 1521 14 29576 0.2 1 27967 1609 15 25117 0.2 1 23397 1720 16 25847 0.2 1 24279 1568 17 22709 0.2 1 21479 1230 18 21119 0.2 1 19963 1156 19 19532 0.2 1 18352 1180 20 18269 0.2 1 17071 1198 21 17315 0.2 1 16162 1153 22 15979 0.2 1 14921 1058 23 14546 0.2 1 13663 883 24 13240 0.2 1 12241 999 25 11561 0.2 1 10799 762 26 9646 0.2 1 8948 698 27 8479 0.2 1 7790 689 28 7753 0.2 1 7178 575 29 6730 0.2 1 6150 580 30 5312 0.2 1 4936 376 31 3881 0.2 1 3564 317 32 3272 0.2 1 3032 240 33 2433 0.2 1 2259 174 34 1382 0.2 1 1284 98 35 876 0.2 1 817 59 36 469 0.2 1 440 29 37 258 0.2 1 234 24 38 153 0.2 1 138 15 39 149 0.2 1 141 8 40 159 0.2 1 146 13 41 199 0.2 1 182 17 42 282 0.2 1 255 27 43 357 0.2 1 330 27 44 764 0.2 1 718 46 45 1062 0.2 1 1014 48 46 1048 0.2 1 988 60 47 823 0.2 1 733 90 48 158 0.2 1 137 21 49 60 0.2 1 52 8 50 78 0.2 1 73 5 51 851 0.2 1 679 172 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/8_ACTTGA_L001_R1_001.fastq.gz ============================================= 14374642 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 104827 (0.7%)