SUMMARISING RUN PARAMETERS ========================== Input filename: 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 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 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 274.83 s (19 us/read; 3.14 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: 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: 425429 (3.0%)