SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_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_15_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1927.93 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 59,408,352 Reads with adapters: 25,824,093 (43.5%) Reads written (passing filters): 59,408,352 (100.0%) Total basepairs processed: 7,517,784,280 bp Quality-trimmed: 2,588,934 bp (0.0%) Total written (filtered): 7,484,679,145 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25824093 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22938238 14852088.0 0 22938238 2 1912707 3713022.0 0 1912707 3 532313 928255.5 0 532313 4 327693 232063.9 0 327693 5 60219 58016.0 0 60219 6 15425 14504.0 0 15425 7 11062 3626.0 0 11062 8 8148 906.5 0 8148 9 2048 226.6 0 1595 453 10 14157 56.7 1 12921 1236 11 179 14.2 1 41 138 12 82 3.5 1 30 52 13 7 0.9 1 1 6 14 28 0.9 1 18 10 15 6 0.9 1 5 1 16 19 0.9 1 13 6 17 3 0.9 1 1 2 18 40 0.9 1 23 17 19 41 0.9 1 30 11 20 7 0.9 1 4 3 21 2 0.9 1 2 22 9 0.9 1 4 5 23 21 0.9 1 15 6 24 24 0.9 1 19 5 25 5 0.9 1 5 26 16 0.9 1 9 7 27 17 0.9 1 14 3 28 2 0.9 1 1 1 29 8 0.9 1 7 1 30 18 0.9 1 10 8 31 27 0.9 1 15 12 32 5 0.9 1 5 33 17 0.9 1 11 6 34 12 0.9 1 8 4 35 15 0.9 1 11 4 36 16 0.9 1 11 5 37 26 0.9 1 19 7 38 8 0.9 1 4 4 39 9 0.9 1 6 3 40 12 0.9 1 8 4 41 16 0.9 1 9 7 42 14 0.9 1 7 7 43 23 0.9 1 18 5 44 21 0.9 1 14 7 45 7 0.9 1 5 2 46 10 0.9 1 7 3 47 12 0.9 1 9 3 48 14 0.9 1 11 3 49 16 0.9 1 13 3 50 8 0.9 1 4 4 51 14 0.9 1 10 4 52 35 0.9 1 20 15 53 5 0.9 1 3 2 54 3 0.9 1 3 55 27 0.9 1 19 8 56 22 0.9 1 17 5 57 4 0.9 1 4 58 8 0.9 1 5 3 59 11 0.9 1 10 1 60 2 0.9 1 1 1 61 5 0.9 1 4 1 62 9 0.9 1 7 2 63 6 0.9 1 5 1 64 4 0.9 1 3 1 65 6 0.9 1 6 66 19 0.9 1 15 4 67 10 0.9 1 9 1 68 8 0.9 1 8 69 14 0.9 1 10 4 70 8 0.9 1 6 2 71 11 0.9 1 11 72 11 0.9 1 9 2 73 9 0.9 1 9 74 15 0.9 1 14 1 75 6 0.9 1 6 76 16 0.9 1 15 1 77 15 0.9 1 11 4 78 12 0.9 1 10 2 79 8 0.9 1 6 2 80 10 0.9 1 8 2 81 13 0.9 1 9 4 82 10 0.9 1 8 2 83 6 0.9 1 6 84 4 0.9 1 4 85 16 0.9 1 12 4 86 7 0.9 1 5 2 87 10 0.9 1 8 2 88 13 0.9 1 12 1 89 9 0.9 1 8 1 90 8 0.9 1 5 3 91 12 0.9 1 8 4 92 15 0.9 1 9 6 93 9 0.9 1 8 1 94 13 0.9 1 9 4 95 6 0.9 1 6 96 14 0.9 1 14 97 14 0.9 1 12 2 98 13 0.9 1 9 4 99 13 0.9 1 11 2 100 8 0.9 1 7 1 101 10 0.9 1 8 2 102 9 0.9 1 6 3 103 7 0.9 1 6 1 104 14 0.9 1 13 1 105 11 0.9 1 9 2 106 21 0.9 1 20 1 107 13 0.9 1 11 2 108 12 0.9 1 9 3 109 13 0.9 1 12 1 110 8 0.9 1 7 1 111 10 0.9 1 8 2 112 17 0.9 1 13 4 113 13 0.9 1 11 2 114 18 0.9 1 16 2 115 9 0.9 1 7 2 116 15 0.9 1 9 6 117 11 0.9 1 11 118 19 0.9 1 17 2 119 22 0.9 1 16 6 120 17 0.9 1 13 4 121 25 0.9 1 24 1 122 29 0.9 1 20 9 123 20 0.9 1 17 3 124 17 0.9 1 16 1 125 18 0.9 1 13 5 126 25 0.9 1 23 2 127 18 0.9 1 15 3 128 26 0.9 1 23 3 129 45 0.9 1 34 11 130 39 0.9 1 32 7 131 30 0.9 1 26 4 132 38 0.9 1 33 5 133 30 0.9 1 24 6 134 40 0.9 1 26 14 135 46 0.9 1 16 30 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R1.fq.gz ============================================= 59408352 sequences processed in total