SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_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_16_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2310.82 s (45 µs/read; 1.35 M reads/minute). === Summary === Total reads processed: 51,910,846 Reads with adapters: 21,719,554 (41.8%) Reads written (passing filters): 51,910,846 (100.0%) Total basepairs processed: 6,471,217,372 bp Quality-trimmed: 2,317,730 bp (0.0%) Total written (filtered): 6,442,864,567 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21719554 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.8% C: 10.3% G: 6.6% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19088005 12977711.5 0 19088005 2 1742115 3244427.9 0 1742115 3 463014 811107.0 0 463014 4 301783 202776.7 0 301783 5 65986 50694.2 0 65986 6 16831 12673.5 0 16831 7 12600 3168.4 0 12600 8 9587 792.1 0 9587 9 2503 198.0 0 2004 499 10 16022 49.5 1 14806 1216 11 172 12.4 1 26 146 12 50 3.1 1 11 39 13 4 0.8 1 0 4 14 3 0.8 1 2 1 15 1 0.8 1 0 1 16 5 0.8 1 2 3 17 3 0.8 1 2 1 18 12 0.8 1 6 6 19 6 0.8 1 3 3 20 2 0.8 1 0 2 21 3 0.8 1 0 3 22 1 0.8 1 0 1 23 3 0.8 1 3 24 2 0.8 1 2 25 1 0.8 1 0 1 26 1 0.8 1 1 27 4 0.8 1 3 1 28 4 0.8 1 3 1 29 5 0.8 1 5 31 2 0.8 1 1 1 33 1 0.8 1 1 34 1 0.8 1 0 1 35 7 0.8 1 3 4 36 2 0.8 1 1 1 37 2 0.8 1 0 2 38 3 0.8 1 2 1 39 5 0.8 1 2 3 40 3 0.8 1 2 1 42 4 0.8 1 1 3 43 2 0.8 1 1 1 44 4 0.8 1 4 45 3 0.8 1 2 1 46 5 0.8 1 3 2 48 7 0.8 1 4 3 49 3 0.8 1 1 2 50 1 0.8 1 1 51 5 0.8 1 3 2 52 3 0.8 1 1 2 53 1 0.8 1 1 54 5 0.8 1 2 3 55 2 0.8 1 1 1 56 1 0.8 1 1 57 2 0.8 1 0 2 58 4 0.8 1 4 59 9 0.8 1 9 60 5 0.8 1 3 2 61 7 0.8 1 3 4 62 6 0.8 1 3 3 63 2 0.8 1 1 1 64 1 0.8 1 0 1 65 6 0.8 1 6 66 6 0.8 1 3 3 67 3 0.8 1 3 68 7 0.8 1 7 69 10 0.8 1 8 2 70 5 0.8 1 4 1 71 6 0.8 1 5 1 72 10 0.8 1 7 3 73 7 0.8 1 6 1 74 5 0.8 1 3 2 75 4 0.8 1 4 76 4 0.8 1 4 77 2 0.8 1 1 1 78 3 0.8 1 2 1 79 5 0.8 1 4 1 80 2 0.8 1 2 81 2 0.8 1 2 82 9 0.8 1 7 2 83 5 0.8 1 5 84 9 0.8 1 7 2 85 3 0.8 1 2 1 86 8 0.8 1 7 1 87 1 0.8 1 1 88 6 0.8 1 5 1 89 4 0.8 1 3 1 90 7 0.8 1 6 1 91 9 0.8 1 8 1 92 8 0.8 1 4 4 93 4 0.8 1 3 1 94 10 0.8 1 9 1 95 7 0.8 1 6 1 96 8 0.8 1 6 2 97 10 0.8 1 8 2 98 16 0.8 1 10 6 99 4 0.8 1 2 2 100 5 0.8 1 4 1 101 9 0.8 1 7 2 102 8 0.8 1 5 3 103 8 0.8 1 8 104 5 0.8 1 4 1 105 4 0.8 1 4 106 10 0.8 1 6 4 107 4 0.8 1 3 1 108 18 0.8 1 12 6 109 15 0.8 1 15 110 14 0.8 1 14 111 15 0.8 1 14 1 112 12 0.8 1 11 1 113 12 0.8 1 12 114 10 0.8 1 8 2 115 6 0.8 1 5 1 116 16 0.8 1 11 5 117 19 0.8 1 17 2 118 9 0.8 1 7 2 119 5 0.8 1 3 2 120 7 0.8 1 6 1 121 15 0.8 1 13 2 122 11 0.8 1 10 1 123 12 0.8 1 10 2 124 12 0.8 1 10 2 125 12 0.8 1 11 1 126 30 0.8 1 27 3 127 14 0.8 1 14 128 14 0.8 1 14 129 17 0.8 1 17 130 15 0.8 1 13 2 131 26 0.8 1 21 5 132 28 0.8 1 23 5 133 25 0.8 1 19 6 134 25 0.8 1 19 6 135 36 0.8 1 14 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R1.fq.gz ============================================= 51910846 sequences processed in total