SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_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_5_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1444.28 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 44,881,631 Reads with adapters: 19,396,540 (43.2%) Reads written (passing filters): 44,881,631 (100.0%) Total basepairs processed: 5,690,565,908 bp Quality-trimmed: 1,400,281 bp (0.0%) Total written (filtered): 5,666,348,897 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19396540 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 6.1% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17327604 11220407.8 0 17327604 2 1345332 2805101.9 0 1345332 3 389691 701275.5 0 389691 4 250075 175318.9 0 250075 5 44626 43829.7 0 44626 6 11196 10957.4 0 11196 7 8027 2739.4 0 8027 8 5938 684.8 0 5938 9 1618 171.2 0 1293 325 10 11157 42.8 1 10293 864 11 122 10.7 1 19 103 12 35 2.7 1 6 29 13 12 0.7 1 5 7 14 4 0.7 1 1 3 15 2 0.7 1 2 16 1 0.7 1 0 1 17 4 0.7 1 3 1 18 2 0.7 1 1 1 19 4 0.7 1 2 2 20 4 0.7 1 2 2 21 3 0.7 1 3 22 4 0.7 1 1 3 23 5 0.7 1 2 3 24 4 0.7 1 3 1 25 4 0.7 1 3 1 26 4 0.7 1 3 1 27 3 0.7 1 3 28 5 0.7 1 2 3 29 2 0.7 1 1 1 30 2 0.7 1 2 31 11 0.7 1 6 5 32 6 0.7 1 3 3 33 8 0.7 1 5 3 34 3 0.7 1 3 35 3 0.7 1 1 2 36 2 0.7 1 2 37 9 0.7 1 6 3 38 7 0.7 1 6 1 39 4 0.7 1 3 1 40 3 0.7 1 3 41 3 0.7 1 1 2 42 1 0.7 1 1 43 3 0.7 1 1 2 44 5 0.7 1 3 2 45 5 0.7 1 5 46 3 0.7 1 3 47 5 0.7 1 5 48 1 0.7 1 1 49 4 0.7 1 4 50 6 0.7 1 4 2 51 7 0.7 1 7 52 3 0.7 1 2 1 53 14 0.7 1 11 3 54 2 0.7 1 2 55 7 0.7 1 5 2 56 7 0.7 1 4 3 57 1 0.7 1 0 1 59 4 0.7 1 4 60 8 0.7 1 5 3 61 2 0.7 1 0 2 62 3 0.7 1 3 63 14 0.7 1 12 2 64 6 0.7 1 6 65 7 0.7 1 7 66 5 0.7 1 5 67 5 0.7 1 2 3 68 6 0.7 1 6 69 14 0.7 1 8 6 70 3 0.7 1 1 2 71 2 0.7 1 2 72 7 0.7 1 6 1 73 1 0.7 1 1 74 6 0.7 1 4 2 75 6 0.7 1 5 1 76 6 0.7 1 3 3 77 6 0.7 1 6 78 8 0.7 1 8 79 6 0.7 1 5 1 80 5 0.7 1 5 81 6 0.7 1 5 1 82 9 0.7 1 7 2 83 10 0.7 1 9 1 84 4 0.7 1 3 1 85 8 0.7 1 7 1 86 3 0.7 1 2 1 87 6 0.7 1 6 88 5 0.7 1 3 2 89 7 0.7 1 7 90 8 0.7 1 7 1 91 4 0.7 1 4 92 9 0.7 1 8 1 93 9 0.7 1 8 1 94 14 0.7 1 12 2 95 12 0.7 1 11 1 96 8 0.7 1 7 1 97 16 0.7 1 16 98 11 0.7 1 8 3 99 14 0.7 1 14 100 13 0.7 1 12 1 101 4 0.7 1 3 1 102 9 0.7 1 8 1 103 12 0.7 1 9 3 104 10 0.7 1 9 1 105 9 0.7 1 7 2 106 8 0.7 1 7 1 107 15 0.7 1 15 108 16 0.7 1 16 109 7 0.7 1 6 1 110 10 0.7 1 9 1 111 12 0.7 1 8 4 112 9 0.7 1 9 113 4 0.7 1 4 114 17 0.7 1 14 3 115 17 0.7 1 13 4 116 12 0.7 1 9 3 117 15 0.7 1 8 7 118 11 0.7 1 10 1 119 22 0.7 1 18 4 120 23 0.7 1 15 8 121 21 0.7 1 16 5 122 14 0.7 1 12 2 123 16 0.7 1 15 1 124 19 0.7 1 17 2 125 21 0.7 1 20 1 126 21 0.7 1 18 3 127 19 0.7 1 14 5 128 28 0.7 1 22 6 129 28 0.7 1 26 2 130 23 0.7 1 22 1 131 19 0.7 1 12 7 132 27 0.7 1 20 7 133 37 0.7 1 30 7 134 28 0.7 1 20 8 135 48 0.7 1 19 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R2.fq.gz ============================================= 44881631 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 44881631 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 187536 (0.42%)