SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_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_8_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1699.97 s (39 µs/read; 1.52 M reads/minute). === Summary === Total reads processed: 43,149,301 Reads with adapters: 18,575,513 (43.0%) Reads written (passing filters): 43,149,301 (100.0%) Total basepairs processed: 5,444,670,140 bp Quality-trimmed: 1,595,123 bp (0.0%) Total written (filtered): 5,421,008,525 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18575513 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.5% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16448696 10787325.2 0 16448696 2 1401414 2696831.3 0 1401414 3 388555 674207.8 0 388555 4 244595 168552.0 0 244595 5 49532 42138.0 0 49532 6 12305 10534.5 0 12305 7 8768 2633.6 0 8768 8 6717 658.4 0 6717 9 1780 164.6 0 1436 344 10 11939 41.2 1 11083 856 11 130 10.3 1 21 109 12 38 2.6 1 12 26 13 8 0.6 1 3 5 14 4 0.6 1 3 1 15 2 0.6 1 1 1 16 7 0.6 1 3 4 17 3 0.6 1 2 1 18 9 0.6 1 6 3 19 15 0.6 1 9 6 20 4 0.6 1 4 21 2 0.6 1 2 22 4 0.6 1 3 1 23 8 0.6 1 5 3 24 2 0.6 1 2 25 3 0.6 1 3 26 4 0.6 1 2 2 27 7 0.6 1 6 1 28 3 0.6 1 2 1 29 6 0.6 1 4 2 30 4 0.6 1 3 1 31 11 0.6 1 6 5 32 3 0.6 1 3 33 5 0.6 1 3 2 34 3 0.6 1 2 1 35 1 0.6 1 0 1 36 2 0.6 1 1 1 37 6 0.6 1 3 3 38 5 0.6 1 4 1 39 2 0.6 1 2 40 3 0.6 1 2 1 41 2 0.6 1 1 1 42 1 0.6 1 1 43 11 0.6 1 7 4 44 4 0.6 1 3 1 45 3 0.6 1 2 1 46 5 0.6 1 3 2 47 4 0.6 1 2 2 48 5 0.6 1 5 49 7 0.6 1 3 4 50 5 0.6 1 3 2 51 4 0.6 1 4 52 3 0.6 1 3 53 7 0.6 1 4 3 54 3 0.6 1 2 1 55 5 0.6 1 5 56 5 0.6 1 3 2 57 9 0.6 1 8 1 58 1 0.6 1 1 59 6 0.6 1 5 1 60 9 0.6 1 6 3 61 4 0.6 1 4 62 7 0.6 1 6 1 63 3 0.6 1 3 64 4 0.6 1 4 65 4 0.6 1 3 1 66 7 0.6 1 6 1 67 2 0.6 1 1 1 68 5 0.6 1 3 2 69 8 0.6 1 5 3 70 6 0.6 1 6 71 3 0.6 1 3 72 13 0.6 1 8 5 73 6 0.6 1 5 1 74 6 0.6 1 4 2 75 9 0.6 1 2 7 76 8 0.6 1 4 4 77 4 0.6 1 4 78 6 0.6 1 6 79 1 0.6 1 1 80 9 0.6 1 5 4 81 6 0.6 1 4 2 82 8 0.6 1 7 1 83 6 0.6 1 4 2 84 7 0.6 1 6 1 85 12 0.6 1 9 3 86 2 0.6 1 1 1 87 4 0.6 1 2 2 88 11 0.6 1 9 2 89 11 0.6 1 10 1 90 12 0.6 1 10 2 91 7 0.6 1 6 1 92 8 0.6 1 7 1 93 7 0.6 1 7 94 8 0.6 1 6 2 95 5 0.6 1 5 96 9 0.6 1 8 1 97 8 0.6 1 5 3 98 3 0.6 1 3 99 6 0.6 1 4 2 100 5 0.6 1 5 101 5 0.6 1 4 1 102 9 0.6 1 5 4 103 5 0.6 1 5 104 9 0.6 1 6 3 105 8 0.6 1 6 2 106 8 0.6 1 6 2 107 10 0.6 1 5 5 108 10 0.6 1 8 2 109 9 0.6 1 7 2 110 7 0.6 1 7 111 11 0.6 1 7 4 112 21 0.6 1 18 3 113 11 0.6 1 9 2 114 11 0.6 1 10 1 115 9 0.6 1 8 1 116 11 0.6 1 8 3 117 20 0.6 1 19 1 118 8 0.6 1 6 2 119 8 0.6 1 7 1 120 11 0.6 1 10 1 121 15 0.6 1 14 1 122 21 0.6 1 16 5 123 17 0.6 1 13 4 124 15 0.6 1 15 125 19 0.6 1 16 3 126 21 0.6 1 19 2 127 23 0.6 1 20 3 128 21 0.6 1 18 3 129 25 0.6 1 21 4 130 23 0.6 1 20 3 131 23 0.6 1 22 1 132 24 0.6 1 21 3 133 37 0.6 1 28 9 134 25 0.6 1 16 9 135 39 0.6 1 14 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R1.fq.gz ============================================= 43149301 sequences processed in total