SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 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 /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --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/data/zr3644_20_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2108.84 s (39 µs/read; 1.55 M reads/minute). === Summary === Total reads processed: 54,311,933 Reads with adapters: 24,163,085 (44.5%) Reads written (passing filters): 54,311,933 (100.0%) Total basepairs processed: 6,898,362,841 bp Quality-trimmed: 4,325,943 bp (0.1%) Total written (filtered): 6,865,728,474 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24163085 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.2% C: 11.4% G: 6.4% T: 37.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21536201 13577983.2 0 21536201 2 1743756 3394495.8 0 1743756 3 527423 848624.0 0 527423 4 276862 212156.0 0 276862 5 40127 53039.0 0 40127 6 11848 13259.7 0 11848 7 8239 3314.9 0 8239 8 5344 828.7 0 5344 9 1714 207.2 0 1298 416 10 10370 51.8 1 9078 1292 11 145 12.9 1 18 127 12 38 3.2 1 3 35 13 12 0.8 1 1 11 15 1 0.8 1 0 1 16 2 0.8 1 0 2 17 3 0.8 1 1 2 18 8 0.8 1 4 4 19 5 0.8 1 2 3 20 3 0.8 1 2 1 21 3 0.8 1 1 2 22 7 0.8 1 4 3 23 2 0.8 1 1 1 24 2 0.8 1 2 25 1 0.8 1 1 26 3 0.8 1 0 3 27 3 0.8 1 2 1 28 4 0.8 1 0 4 29 2 0.8 1 1 1 30 3 0.8 1 2 1 31 3 0.8 1 1 2 32 5 0.8 1 2 3 33 2 0.8 1 2 34 3 0.8 1 2 1 35 2 0.8 1 2 36 2 0.8 1 2 37 1 0.8 1 0 1 38 2 0.8 1 1 1 39 3 0.8 1 3 40 2 0.8 1 2 41 6 0.8 1 5 1 42 4 0.8 1 2 2 43 5 0.8 1 3 2 44 3 0.8 1 3 45 4 0.8 1 3 1 46 2 0.8 1 1 1 47 4 0.8 1 1 3 48 2 0.8 1 2 49 1 0.8 1 0 1 50 8 0.8 1 8 51 4 0.8 1 4 52 4 0.8 1 4 53 5 0.8 1 4 1 54 4 0.8 1 3 1 55 3 0.8 1 3 56 2 0.8 1 2 57 4 0.8 1 2 2 58 3 0.8 1 1 2 59 1 0.8 1 0 1 60 5 0.8 1 2 3 61 4 0.8 1 2 2 62 5 0.8 1 4 1 63 6 0.8 1 6 64 6 0.8 1 5 1 65 2 0.8 1 0 2 66 4 0.8 1 2 2 67 2 0.8 1 2 68 1 0.8 1 1 69 7 0.8 1 5 2 70 1 0.8 1 0 1 71 3 0.8 1 3 72 6 0.8 1 5 1 73 3 0.8 1 1 2 74 7 0.8 1 6 1 75 2 0.8 1 1 1 76 8 0.8 1 7 1 77 3 0.8 1 1 2 78 3 0.8 1 3 79 11 0.8 1 8 3 80 3 0.8 1 3 81 8 0.8 1 7 1 82 2 0.8 1 1 1 83 10 0.8 1 5 5 84 13 0.8 1 13 85 5 0.8 1 2 3 86 3 0.8 1 1 2 87 5 0.8 1 2 3 88 8 0.8 1 5 3 89 13 0.8 1 13 90 9 0.8 1 8 1 91 7 0.8 1 5 2 92 6 0.8 1 5 1 93 4 0.8 1 2 2 94 3 0.8 1 2 1 95 6 0.8 1 6 96 7 0.8 1 5 2 97 6 0.8 1 6 98 7 0.8 1 7 99 5 0.8 1 1 4 100 12 0.8 1 11 1 101 8 0.8 1 7 1 102 10 0.8 1 7 3 103 12 0.8 1 10 2 104 8 0.8 1 7 1 105 10 0.8 1 8 2 106 10 0.8 1 9 1 107 4 0.8 1 4 108 8 0.8 1 6 2 109 9 0.8 1 9 110 6 0.8 1 5 1 111 21 0.8 1 12 9 112 15 0.8 1 14 1 113 14 0.8 1 13 1 114 11 0.8 1 10 1 115 14 0.8 1 12 2 116 9 0.8 1 9 117 13 0.8 1 11 2 118 20 0.8 1 15 5 119 22 0.8 1 21 1 120 18 0.8 1 17 1 121 17 0.8 1 12 5 122 15 0.8 1 10 5 123 19 0.8 1 17 2 124 25 0.8 1 18 7 125 20 0.8 1 14 6 126 22 0.8 1 19 3 127 24 0.8 1 20 4 128 27 0.8 1 23 4 129 28 0.8 1 24 4 130 19 0.8 1 16 3 131 30 0.8 1 20 10 132 32 0.8 1 27 5 133 40 0.8 1 34 6 134 29 0.8 1 20 9 135 40 0.8 1 18 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.fq.gz ============================================= 54311933 sequences processed in total