SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2 --threads 28 Output file will be GZIP compressed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1473.86 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 54,032,664 Reads with adapters: 23,593,118 (43.7%) Reads written (passing filters): 54,032,664 (100.0%) Total basepairs processed: 5,745,290,893 bp Quality-trimmed: 7,309,874 bp (0.1%) Total written (filtered): 5,711,425,985 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23593118 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.3% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21565962 13508166.0 0 21565962 2 1323130 3377041.5 0 1323130 3 481295 844260.4 0 481295 4 219675 211065.1 0 219675 5 1549 52766.3 0 1549 6 491 13191.6 0 491 7 149 3297.9 0 149 8 40 824.5 0 40 9 238 206.1 0 21 217 10 484 51.5 1 2 482 11 92 12.9 1 0 92 12 8 3.2 1 0 8 13 2 0.8 1 0 2 15 1 0.8 1 0 1 17 1 0.8 1 0 1 25 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz ============================================= 54032664 sequences processed in total