SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_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_5_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1590.82 s (35 µs/read; 1.69 M reads/minute). === Summary === Total reads processed: 44,881,631 Reads with adapters: 19,722,224 (43.9%) Reads written (passing filters): 44,881,631 (100.0%) Total basepairs processed: 5,692,356,532 bp Quality-trimmed: 2,683,556 bp (0.0%) Total written (filtered): 5,666,410,901 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19722224 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.7% C: 10.8% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17528792 11220407.8 0 17528792 2 1454610 2805101.9 0 1454610 3 418340 701275.5 0 418340 4 240375 175318.9 0 240375 5 41021 43829.7 0 41021 6 11374 10957.4 0 11374 7 7886 2739.4 0 7886 8 5720 684.8 0 5720 9 1679 171.2 0 1298 381 10 11099 42.8 1 10017 1082 11 132 10.7 1 24 108 12 49 2.7 1 16 33 13 7 0.7 1 2 5 14 10 0.7 1 3 7 15 2 0.7 1 1 1 16 11 0.7 1 9 2 17 1 0.7 1 0 1 18 12 0.7 1 6 6 19 15 0.7 1 9 6 20 3 0.7 1 1 2 21 3 0.7 1 1 2 22 4 0.7 1 2 2 23 8 0.7 1 7 1 24 4 0.7 1 4 25 2 0.7 1 1 1 26 6 0.7 1 4 2 27 10 0.7 1 7 3 28 5 0.7 1 2 3 29 5 0.7 1 4 1 30 6 0.7 1 2 4 31 6 0.7 1 4 2 32 5 0.7 1 4 1 33 8 0.7 1 4 4 34 2 0.7 1 0 2 35 6 0.7 1 4 2 36 11 0.7 1 5 6 37 3 0.7 1 2 1 38 8 0.7 1 5 3 39 6 0.7 1 6 40 3 0.7 1 3 41 4 0.7 1 2 2 42 4 0.7 1 3 1 43 8 0.7 1 7 1 44 9 0.7 1 7 2 45 3 0.7 1 2 1 46 7 0.7 1 3 4 47 2 0.7 1 1 1 48 6 0.7 1 4 2 49 11 0.7 1 7 4 50 5 0.7 1 5 51 4 0.7 1 3 1 52 8 0.7 1 5 3 53 6 0.7 1 4 2 54 4 0.7 1 3 1 55 11 0.7 1 8 3 56 7 0.7 1 3 4 57 4 0.7 1 4 58 3 0.7 1 2 1 59 6 0.7 1 5 1 61 3 0.7 1 1 2 62 5 0.7 1 5 63 3 0.7 1 3 64 2 0.7 1 2 65 7 0.7 1 5 2 66 6 0.7 1 4 2 67 6 0.7 1 6 68 5 0.7 1 5 69 4 0.7 1 4 70 2 0.7 1 2 71 2 0.7 1 1 1 72 3 0.7 1 3 73 9 0.7 1 8 1 74 8 0.7 1 4 4 75 6 0.7 1 6 76 11 0.7 1 10 1 77 3 0.7 1 2 1 78 11 0.7 1 7 4 79 6 0.7 1 5 1 81 2 0.7 1 2 82 9 0.7 1 7 2 83 7 0.7 1 7 84 6 0.7 1 3 3 85 8 0.7 1 8 86 9 0.7 1 6 3 87 12 0.7 1 11 1 88 4 0.7 1 3 1 89 9 0.7 1 8 1 90 13 0.7 1 13 91 4 0.7 1 4 92 7 0.7 1 5 2 93 3 0.7 1 3 94 8 0.7 1 7 1 95 9 0.7 1 9 96 10 0.7 1 9 1 97 9 0.7 1 8 1 98 13 0.7 1 11 2 99 14 0.7 1 11 3 100 14 0.7 1 13 1 101 8 0.7 1 5 3 102 11 0.7 1 10 1 103 7 0.7 1 6 1 104 10 0.7 1 9 1 105 8 0.7 1 7 1 106 7 0.7 1 6 1 107 12 0.7 1 11 1 108 10 0.7 1 10 109 10 0.7 1 9 1 110 18 0.7 1 16 2 111 14 0.7 1 13 1 112 14 0.7 1 11 3 113 13 0.7 1 11 2 114 13 0.7 1 9 4 115 13 0.7 1 10 3 116 4 0.7 1 3 1 117 10 0.7 1 8 2 118 12 0.7 1 10 2 119 14 0.7 1 11 3 120 12 0.7 1 12 121 21 0.7 1 17 4 122 17 0.7 1 16 1 123 15 0.7 1 9 6 124 22 0.7 1 21 1 125 12 0.7 1 12 126 33 0.7 1 28 5 127 27 0.7 1 22 5 128 30 0.7 1 26 4 129 26 0.7 1 22 4 130 28 0.7 1 25 3 131 26 0.7 1 20 6 132 26 0.7 1 24 2 133 27 0.7 1 19 8 134 28 0.7 1 18 10 135 33 0.7 1 15 18 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R1.fq.gz ============================================= 44881631 sequences processed in total