SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_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_24_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1728.47 s (33 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 53,154,280 Reads with adapters: 23,096,436 (43.5%) Reads written (passing filters): 53,154,280 (100.0%) Total basepairs processed: 6,723,235,587 bp Quality-trimmed: 2,278,769 bp (0.0%) Total written (filtered): 6,693,671,857 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23096436 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% 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 20502045 13288570.0 0 20502045 2 1722172 3322142.5 0 1722172 3 475946 830535.6 0 475946 4 293396 207633.9 0 293396 5 54450 51908.5 0 54450 6 14073 12977.1 0 14073 7 10189 3244.3 0 10189 8 7696 811.1 0 7696 9 2014 202.8 0 1595 419 10 13015 50.7 1 11941 1074 11 181 12.7 1 26 155 12 66 3.2 1 19 47 13 6 0.8 1 1 5 14 24 0.8 1 17 7 15 4 0.8 1 3 1 16 14 0.8 1 8 6 17 2 0.8 1 1 1 18 21 0.8 1 8 13 19 26 0.8 1 11 15 20 2 0.8 1 2 21 1 0.8 1 1 22 8 0.8 1 5 3 23 19 0.8 1 10 9 24 22 0.8 1 16 6 25 4 0.8 1 2 2 26 13 0.8 1 9 4 27 9 0.8 1 9 29 7 0.8 1 3 4 30 13 0.8 1 7 6 31 12 0.8 1 9 3 32 4 0.8 1 2 2 33 18 0.8 1 9 9 34 2 0.8 1 1 1 35 6 0.8 1 5 1 36 9 0.8 1 7 2 37 17 0.8 1 10 7 38 6 0.8 1 5 1 39 7 0.8 1 6 1 40 11 0.8 1 8 3 41 11 0.8 1 6 5 42 9 0.8 1 7 2 43 9 0.8 1 6 3 44 11 0.8 1 7 4 45 3 0.8 1 1 2 46 10 0.8 1 5 5 47 4 0.8 1 2 2 48 17 0.8 1 12 5 49 11 0.8 1 4 7 50 6 0.8 1 3 3 51 5 0.8 1 3 2 52 11 0.8 1 11 53 5 0.8 1 5 54 6 0.8 1 6 55 12 0.8 1 7 5 56 10 0.8 1 8 2 57 5 0.8 1 5 58 2 0.8 1 2 59 10 0.8 1 9 1 60 4 0.8 1 3 1 61 3 0.8 1 2 1 62 12 0.8 1 8 4 63 1 0.8 1 1 64 3 0.8 1 1 2 66 13 0.8 1 11 2 67 8 0.8 1 7 1 68 9 0.8 1 8 1 69 5 0.8 1 2 3 70 5 0.8 1 5 71 10 0.8 1 6 4 72 7 0.8 1 5 2 73 5 0.8 1 4 1 74 2 0.8 1 2 75 8 0.8 1 7 1 76 2 0.8 1 1 1 77 9 0.8 1 7 2 78 8 0.8 1 6 2 79 1 0.8 1 0 1 80 5 0.8 1 4 1 81 6 0.8 1 4 2 82 7 0.8 1 5 2 83 2 0.8 1 1 1 84 4 0.8 1 4 85 7 0.8 1 7 86 6 0.8 1 5 1 87 10 0.8 1 9 1 88 5 0.8 1 4 1 89 11 0.8 1 9 2 90 8 0.8 1 7 1 91 6 0.8 1 5 1 92 8 0.8 1 6 2 93 4 0.8 1 4 94 3 0.8 1 3 95 4 0.8 1 4 96 6 0.8 1 6 97 4 0.8 1 4 98 7 0.8 1 7 99 4 0.8 1 4 100 6 0.8 1 4 2 101 7 0.8 1 7 102 4 0.8 1 1 3 103 6 0.8 1 6 104 5 0.8 1 4 1 105 7 0.8 1 7 106 8 0.8 1 7 1 107 16 0.8 1 11 5 108 17 0.8 1 12 5 109 15 0.8 1 10 5 110 6 0.8 1 5 1 111 5 0.8 1 4 1 112 11 0.8 1 11 113 13 0.8 1 10 3 114 11 0.8 1 9 2 115 8 0.8 1 5 3 116 5 0.8 1 5 117 8 0.8 1 6 2 118 10 0.8 1 7 3 119 12 0.8 1 10 2 120 15 0.8 1 14 1 121 26 0.8 1 22 4 122 26 0.8 1 21 5 123 9 0.8 1 6 3 124 19 0.8 1 16 3 125 19 0.8 1 13 6 126 15 0.8 1 15 127 13 0.8 1 12 1 128 29 0.8 1 26 3 129 32 0.8 1 29 3 130 12 0.8 1 10 2 131 22 0.8 1 20 2 132 31 0.8 1 26 5 133 22 0.8 1 18 4 134 16 0.8 1 12 4 135 31 0.8 1 15 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R1.fq.gz ============================================= 53154280 sequences processed in total