SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_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_1_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1887.98 s (36 µs/read; 1.66 M reads/minute). === Summary === Total reads processed: 52,225,074 Reads with adapters: 22,053,906 (42.2%) Reads written (passing filters): 52,225,074 (100.0%) Total basepairs processed: 6,553,667,817 bp Quality-trimmed: 1,729,636 bp (0.0%) Total written (filtered): 6,525,541,768 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22053906 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.2% G: 6.6% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19424719 13056268.5 0 19424719 2 1730165 3264067.1 0 1730165 3 461077 816016.8 0 461077 4 305022 204004.2 0 305022 5 70710 51001.0 0 70710 6 17504 12750.3 0 17504 7 12989 3187.6 0 12989 8 10246 796.9 0 10246 9 2676 199.2 0 2190 486 10 17881 49.8 1 16641 1240 11 149 12.5 1 16 133 12 40 3.1 1 8 32 13 4 0.8 1 1 3 14 1 0.8 1 0 1 16 3 0.8 1 1 2 17 2 0.8 1 1 1 18 6 0.8 1 1 5 19 5 0.8 1 2 3 20 1 0.8 1 0 1 21 2 0.8 1 0 2 22 4 0.8 1 0 4 23 4 0.8 1 2 2 24 1 0.8 1 1 25 4 0.8 1 2 2 26 2 0.8 1 1 1 27 4 0.8 1 0 4 28 2 0.8 1 0 2 29 2 0.8 1 1 1 30 3 0.8 1 0 3 31 3 0.8 1 2 1 32 2 0.8 1 0 2 33 3 0.8 1 2 1 34 1 0.8 1 0 1 35 5 0.8 1 5 36 1 0.8 1 1 38 2 0.8 1 2 39 5 0.8 1 2 3 40 3 0.8 1 2 1 41 2 0.8 1 0 2 42 2 0.8 1 2 43 2 0.8 1 1 1 44 2 0.8 1 1 1 45 2 0.8 1 2 46 3 0.8 1 1 2 47 1 0.8 1 1 48 3 0.8 1 1 2 49 8 0.8 1 7 1 50 3 0.8 1 3 52 1 0.8 1 1 53 2 0.8 1 0 2 54 3 0.8 1 2 1 55 2 0.8 1 0 2 56 6 0.8 1 3 3 57 2 0.8 1 2 58 3 0.8 1 2 1 59 2 0.8 1 2 60 2 0.8 1 2 61 1 0.8 1 1 62 2 0.8 1 2 63 1 0.8 1 1 64 4 0.8 1 2 2 65 3 0.8 1 2 1 66 11 0.8 1 9 2 67 3 0.8 1 3 68 2 0.8 1 1 1 70 2 0.8 1 2 71 3 0.8 1 1 2 72 7 0.8 1 7 73 2 0.8 1 1 1 74 6 0.8 1 3 3 75 3 0.8 1 2 1 76 4 0.8 1 3 1 77 1 0.8 1 1 78 4 0.8 1 4 79 4 0.8 1 3 1 80 5 0.8 1 5 81 4 0.8 1 3 1 82 2 0.8 1 2 83 4 0.8 1 4 84 6 0.8 1 6 85 3 0.8 1 2 1 86 5 0.8 1 2 3 87 4 0.8 1 2 2 88 2 0.8 1 2 89 1 0.8 1 0 1 90 2 0.8 1 0 2 91 8 0.8 1 8 92 8 0.8 1 7 1 93 3 0.8 1 2 1 94 5 0.8 1 5 95 11 0.8 1 10 1 96 10 0.8 1 5 5 97 7 0.8 1 3 4 98 11 0.8 1 9 2 99 7 0.8 1 7 100 5 0.8 1 4 1 101 6 0.8 1 5 1 102 5 0.8 1 4 1 103 4 0.8 1 3 1 104 5 0.8 1 2 3 105 8 0.8 1 8 106 4 0.8 1 4 107 13 0.8 1 11 2 108 12 0.8 1 10 2 109 3 0.8 1 3 110 12 0.8 1 10 2 111 9 0.8 1 6 3 112 4 0.8 1 1 3 113 11 0.8 1 8 3 114 12 0.8 1 11 1 115 4 0.8 1 3 1 116 10 0.8 1 9 1 117 10 0.8 1 8 2 118 8 0.8 1 5 3 119 20 0.8 1 14 6 120 14 0.8 1 10 4 121 11 0.8 1 9 2 122 10 0.8 1 6 4 123 7 0.8 1 6 1 124 10 0.8 1 6 4 125 15 0.8 1 13 2 126 11 0.8 1 11 127 6 0.8 1 5 1 128 15 0.8 1 13 2 129 17 0.8 1 12 5 130 24 0.8 1 20 4 131 23 0.8 1 21 2 132 19 0.8 1 18 1 133 25 0.8 1 20 5 134 29 0.8 1 24 5 135 30 0.8 1 15 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R1.fq.gz ============================================= 52225074 sequences processed in total