SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/7_CAGATC_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/7_CAGATC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 190.31 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 10,295,293 Reads with adapters: 4,013,389 (39.0%) Reads written (passing filters): 10,295,293 (100.0%) Total basepairs processed: 525,059,943 bp Quality-trimmed: 1,586,339 bp (0.3%) Total written (filtered): 514,717,887 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4013389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 1.5% G: 21.0% T: 46.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2753314 2573823.2 0 2753314 2 652174 643455.8 0 652174 3 234852 160864.0 0 234852 4 103251 40216.0 0 103251 5 24247 10054.0 0 24247 6 21578 2513.5 0 21578 7 19539 628.4 0 19539 8 18333 157.1 0 18333 9 18085 39.3 0 17813 272 10 16281 9.8 1 15449 832 11 15275 2.5 1 14558 717 12 14364 0.6 1 13780 584 13 12550 0.2 1 12015 535 14 12626 0.2 1 12023 603 15 11002 0.2 1 10360 642 16 10624 0.2 1 10072 552 17 9315 0.2 1 8892 423 18 8494 0.2 1 8140 354 19 7724 0.2 1 7315 409 20 6985 0.2 1 6624 361 21 6391 0.2 1 6101 290 22 5631 0.2 1 5324 307 23 5161 0.2 1 4876 285 24 4535 0.2 1 4266 269 25 3712 0.2 1 3500 212 26 3101 0.2 1 2926 175 27 2667 0.2 1 2470 197 28 2496 0.2 1 2324 172 29 2116 0.2 1 1986 130 30 1597 0.2 1 1488 109 31 1151 0.2 1 1078 73 32 928 0.2 1 863 65 33 646 0.2 1 616 30 34 388 0.2 1 362 26 35 261 0.2 1 247 14 36 164 0.2 1 147 17 37 73 0.2 1 61 12 38 53 0.2 1 49 4 39 55 0.2 1 50 5 40 49 0.2 1 47 2 41 44 0.2 1 41 3 42 89 0.2 1 82 7 43 89 0.2 1 81 8 44 185 0.2 1 169 16 45 288 0.2 1 271 17 46 364 0.2 1 350 14 47 232 0.2 1 213 19 48 33 0.2 1 28 5 49 15 0.2 1 14 1 50 21 0.2 1 15 6 51 241 0.2 1 199 42 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/7_CAGATC_L001_R1_001.fastq.gz ============================================= 10295293 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 42102 (0.4%)