SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_6_s456.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 zr1394_6_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 934.29 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 46,944,411 Reads with adapters: 19,526,974 (41.6%) Reads written (passing filters): 46,944,411 (100.0%) Total basepairs processed: 2,363,416,290 bp Quality-trimmed: 2,138,751 bp (0.1%) Total written (filtered): 2,340,634,139 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19526974 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.4% C: 10.6% G: 3.2% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18794438 11736102.8 0 18794438 2 469350 2934025.7 0 469350 3 205047 733506.4 0 205047 4 46939 183376.6 0 46939 5 4257 45844.2 0 4257 6 546 11461.0 0 546 7 1292 2865.3 0 1292 8 569 716.3 0 569 9 311 179.1 0 31 280 10 633 44.8 1 10 623 11 287 11.2 1 35 252 12 205 2.8 1 1 204 13 93 0.7 1 0 93 14 89 0.7 1 0 89 15 163 0.7 1 0 163 16 366 0.7 1 0 366 17 1103 0.7 1 0 1103 18 992 0.7 1 0 992 19 108 0.7 1 0 108 20 16 0.7 1 0 16 21 11 0.7 1 0 11 22 7 0.7 1 0 7 23 9 0.7 1 0 9 24 12 0.7 1 0 12 25 16 0.7 1 0 16 26 23 0.7 1 0 23 27 13 0.7 1 0 13 28 8 0.7 1 0 8 29 6 0.7 1 0 6 30 14 0.7 1 0 14 31 8 0.7 1 0 8 32 13 0.7 1 0 13 33 13 0.7 1 0 13 34 12 0.7 1 0 12 35 4 0.7 1 0 4 39 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_6_s456.fastq.gz ============================================= 46944411 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 489263 (1.0%)