SUMMARISING RUN PARAMETERS ========================== Input filename: 2_CGATGT_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 2_CGATGT_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 229.58 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 11,954,873 Reads with adapters: 4,759,817 (39.8%) Reads written (passing filters): 11,954,873 (100.0%) Total basepairs processed: 609,698,523 bp Quality-trimmed: 1,934,183 bp (0.3%) Total written (filtered): 595,521,684 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4759817 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 2.2% G: 21.7% T: 45.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3158682 2988718.2 0 3158682 2 762522 747179.6 0 762522 3 283079 186794.9 0 283079 4 123149 46698.7 0 123149 5 33918 11674.7 0 33918 6 29520 2918.7 0 29520 7 26966 729.7 0 26966 8 26048 182.4 0 26048 9 26083 45.6 0 25757 326 10 23691 11.4 1 22611 1080 11 22687 2.9 1 21775 912 12 21992 0.7 1 21251 741 13 18838 0.2 1 18122 716 14 19991 0.2 1 19139 852 15 18228 0.2 1 17261 967 16 17515 0.2 1 16720 795 17 15543 0.2 1 14889 654 18 14803 0.2 1 14230 573 19 13744 0.2 1 13084 660 20 13268 0.2 1 12580 688 21 12071 0.2 1 11465 606 22 11254 0.2 1 10660 594 23 10146 0.2 1 9659 487 24 9365 0.2 1 8841 524 25 8059 0.2 1 7635 424 26 6645 0.2 1 6261 384 27 5757 0.2 1 5367 390 28 5293 0.2 1 4964 329 29 4478 0.2 1 4163 315 30 3459 0.2 1 3247 212 31 2708 0.2 1 2539 169 32 2250 0.2 1 2116 134 33 1610 0.2 1 1520 90 34 928 0.2 1 877 51 35 581 0.2 1 549 32 36 282 0.2 1 264 18 37 181 0.2 1 171 10 38 146 0.2 1 128 18 39 111 0.2 1 103 8 40 90 0.2 1 79 11 41 136 0.2 1 133 3 42 230 0.2 1 218 12 43 275 0.2 1 260 15 44 517 0.2 1 497 20 45 700 0.2 1 669 31 46 841 0.2 1 800 41 47 561 0.2 1 499 62 48 119 0.2 1 109 10 49 54 0.2 1 47 7 50 67 0.2 1 59 8 51 636 0.2 1 513 123 RUN STATISTICS FOR INPUT FILE: 2_CGATGT_L001_R1_001.fastq.gz ============================================= 11954873 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 300406 (2.5%)