SUMMARISING RUN PARAMETERS ========================== Input filename: 5_ACAGTG_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 10 bp from their 5' end to avoid poor qualities or biases All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 5_ACAGTG_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 241.78 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 12,589,609 Reads with adapters: 5,003,685 (39.7%) Reads written (passing filters): 12,589,609 (100.0%) Total basepairs processed: 642,070,059 bp Quality-trimmed: 2,594,232 bp (0.4%) Total written (filtered): 626,202,947 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5003685 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 2.0% G: 21.9% T: 45.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3295604 3147402.2 0 3295604 2 802076 786850.6 0 802076 3 289174 196712.6 0 289174 4 132748 49178.2 0 132748 5 37772 12294.5 0 37772 6 33518 3073.6 0 33518 7 30685 768.4 0 30685 8 29675 192.1 0 29675 9 29294 48.0 0 28914 380 10 26932 12.0 1 25771 1161 11 25424 3.0 1 24438 986 12 24576 0.8 1 23687 889 13 21216 0.2 1 20361 855 14 22921 0.2 1 21965 956 15 18687 0.2 1 17712 975 16 19766 0.2 1 18777 989 17 16813 0.2 1 16133 680 18 16135 0.2 1 15502 633 19 15003 0.2 1 14260 743 20 13995 0.2 1 13335 660 21 12979 0.2 1 12295 684 22 12172 0.2 1 11539 633 23 11217 0.2 1 10663 554 24 10242 0.2 1 9608 634 25 8811 0.2 1 8346 465 26 7468 0.2 1 7010 458 27 6717 0.2 1 6246 471 28 6216 0.2 1 5834 382 29 5562 0.2 1 5215 347 30 4179 0.2 1 3933 246 31 3458 0.2 1 3263 195 32 2742 0.2 1 2590 152 33 2233 0.2 1 2128 105 34 1264 0.2 1 1197 67 35 813 0.2 1 766 47 36 417 0.2 1 393 24 37 250 0.2 1 236 14 38 182 0.2 1 174 8 39 98 0.2 1 94 4 40 96 0.2 1 94 2 41 112 0.2 1 107 5 42 235 0.2 1 225 10 43 281 0.2 1 265 16 44 521 0.2 1 505 16 45 769 0.2 1 747 22 46 900 0.2 1 865 35 47 653 0.2 1 593 60 48 123 0.2 1 117 6 49 71 0.2 1 63 8 50 66 0.2 1 62 4 51 824 0.2 1 707 117 RUN STATISTICS FOR INPUT FILE: 5_ACAGTG_L001_R1_001.fastq.gz ============================================= 12589609 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 358290 (2.8%)