SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.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_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1684.20 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 51,910,846 Reads with adapters: 21,601,645 (41.6%) Reads written (passing filters): 51,910,846 (100.0%) Total basepairs processed: 6,469,595,542 bp Quality-trimmed: 2,140,341 bp (0.0%) Total written (filtered): 6,441,680,830 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21601645 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.1% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19110675 12977711.5 0 19110675 2 1612493 3244427.9 0 1612493 3 445905 811107.0 0 445905 4 308602 202776.7 0 308602 5 66386 50694.2 0 66386 6 16416 12673.5 0 16416 7 12511 3168.4 0 12511 8 9358 792.1 0 9358 9 2445 198.0 0 2039 406 10 15613 49.5 1 14455 1158 11 193 12.4 1 35 158 12 47 3.1 1 7 40 13 2 0.8 1 0 2 14 10 0.8 1 3 7 15 3 0.8 1 1 2 16 7 0.8 1 1 6 17 2 0.8 1 1 1 18 6 0.8 1 2 4 19 17 0.8 1 8 9 20 1 0.8 1 1 21 2 0.8 1 0 2 22 6 0.8 1 4 2 23 8 0.8 1 6 2 24 6 0.8 1 3 3 25 2 0.8 1 0 2 26 2 0.8 1 2 27 3 0.8 1 1 2 28 7 0.8 1 4 3 29 1 0.8 1 0 1 30 1 0.8 1 0 1 31 1 0.8 1 1 32 7 0.8 1 3 4 33 1 0.8 1 1 34 5 0.8 1 5 35 5 0.8 1 3 2 36 6 0.8 1 6 37 5 0.8 1 4 1 38 3 0.8 1 1 2 39 9 0.8 1 5 4 40 3 0.8 1 3 41 1 0.8 1 1 42 4 0.8 1 2 2 43 2 0.8 1 1 1 44 5 0.8 1 2 3 45 2 0.8 1 1 1 46 6 0.8 1 4 2 47 7 0.8 1 5 2 48 2 0.8 1 0 2 49 3 0.8 1 1 2 50 3 0.8 1 1 2 51 6 0.8 1 5 1 52 3 0.8 1 3 53 6 0.8 1 5 1 54 9 0.8 1 5 4 55 8 0.8 1 6 2 56 3 0.8 1 2 1 57 8 0.8 1 8 58 5 0.8 1 4 1 59 5 0.8 1 5 60 4 0.8 1 2 2 61 3 0.8 1 2 1 62 8 0.8 1 5 3 63 10 0.8 1 8 2 64 5 0.8 1 3 2 65 10 0.8 1 9 1 66 2 0.8 1 1 1 67 4 0.8 1 3 1 68 5 0.8 1 3 2 69 5 0.8 1 4 1 70 1 0.8 1 1 71 10 0.8 1 9 1 72 2 0.8 1 1 1 73 4 0.8 1 3 1 74 8 0.8 1 5 3 75 10 0.8 1 9 1 76 3 0.8 1 2 1 77 6 0.8 1 6 78 7 0.8 1 7 79 11 0.8 1 8 3 80 7 0.8 1 6 1 81 6 0.8 1 4 2 82 9 0.8 1 5 4 83 11 0.8 1 9 2 84 8 0.8 1 7 1 85 3 0.8 1 3 86 2 0.8 1 1 1 87 5 0.8 1 5 88 5 0.8 1 3 2 89 4 0.8 1 3 1 90 8 0.8 1 8 91 11 0.8 1 9 2 92 1 0.8 1 1 93 7 0.8 1 3 4 94 8 0.8 1 7 1 95 8 0.8 1 5 3 96 5 0.8 1 4 1 97 5 0.8 1 4 1 98 4 0.8 1 3 1 99 13 0.8 1 10 3 100 15 0.8 1 11 4 101 3 0.8 1 3 102 10 0.8 1 10 103 8 0.8 1 5 3 104 14 0.8 1 10 4 105 3 0.8 1 3 106 6 0.8 1 6 107 14 0.8 1 13 1 108 6 0.8 1 6 109 7 0.8 1 6 1 110 12 0.8 1 9 3 111 13 0.8 1 10 3 112 8 0.8 1 7 1 113 13 0.8 1 11 2 114 10 0.8 1 8 2 115 10 0.8 1 9 1 116 13 0.8 1 11 2 117 8 0.8 1 6 2 118 14 0.8 1 12 2 119 17 0.8 1 16 1 120 22 0.8 1 19 3 121 6 0.8 1 5 1 122 13 0.8 1 12 1 123 14 0.8 1 13 1 124 11 0.8 1 8 3 125 10 0.8 1 9 1 126 15 0.8 1 14 1 127 18 0.8 1 16 2 128 22 0.8 1 20 2 129 23 0.8 1 17 6 130 24 0.8 1 21 3 131 28 0.8 1 25 3 132 29 0.8 1 25 4 133 29 0.8 1 20 9 134 31 0.8 1 21 10 135 35 0.8 1 12 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.fq.gz ============================================= 51910846 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 51910846 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 294893 (0.57%)