SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_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_10_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2087.48 s (39 µs/read; 1.52 M reads/minute). === Summary === Total reads processed: 52,847,841 Reads with adapters: 22,764,641 (43.1%) Reads written (passing filters): 52,847,841 (100.0%) Total basepairs processed: 6,663,716,444 bp Quality-trimmed: 2,077,880 bp (0.0%) Total written (filtered): 6,634,572,674 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22764641 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.4% G: 6.5% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20139970 13211960.2 0 20139970 2 1741524 3302990.1 0 1741524 3 474041 825747.5 0 474041 4 299082 206436.9 0 299082 5 57704 51609.2 0 57704 6 15545 12902.3 0 15545 7 10772 3225.6 0 10772 8 8021 806.4 0 8021 9 2063 201.6 0 1607 456 10 13825 50.4 1 12748 1077 11 200 12.6 1 31 169 12 82 3.1 1 29 53 13 7 0.8 1 1 6 14 28 0.8 1 19 9 15 8 0.8 1 2 6 16 21 0.8 1 14 7 17 4 0.8 1 3 1 18 34 0.8 1 21 13 19 37 0.8 1 23 14 20 6 0.8 1 5 1 21 4 0.8 1 4 22 9 0.8 1 7 2 23 23 0.8 1 18 5 24 37 0.8 1 22 15 25 5 0.8 1 4 1 26 16 0.8 1 12 4 27 18 0.8 1 15 3 28 5 0.8 1 5 29 14 0.8 1 12 2 30 20 0.8 1 9 11 31 29 0.8 1 23 6 32 8 0.8 1 7 1 33 26 0.8 1 19 7 34 6 0.8 1 4 2 35 15 0.8 1 13 2 36 9 0.8 1 5 4 37 17 0.8 1 12 5 38 17 0.8 1 16 1 39 11 0.8 1 7 4 40 12 0.8 1 9 3 41 12 0.8 1 8 4 42 17 0.8 1 10 7 43 15 0.8 1 12 3 44 19 0.8 1 14 5 45 8 0.8 1 6 2 46 8 0.8 1 7 1 47 3 0.8 1 3 48 20 0.8 1 13 7 49 13 0.8 1 10 3 50 9 0.8 1 7 2 51 11 0.8 1 9 2 52 18 0.8 1 14 4 53 10 0.8 1 6 4 54 6 0.8 1 6 55 25 0.8 1 17 8 56 18 0.8 1 15 3 57 12 0.8 1 10 2 58 7 0.8 1 5 2 59 14 0.8 1 12 2 60 5 0.8 1 2 3 61 11 0.8 1 11 62 16 0.8 1 15 1 63 6 0.8 1 5 1 64 9 0.8 1 8 1 65 10 0.8 1 9 1 66 16 0.8 1 11 5 67 8 0.8 1 8 68 9 0.8 1 7 2 69 12 0.8 1 8 4 70 11 0.8 1 10 1 71 12 0.8 1 12 72 10 0.8 1 7 3 73 6 0.8 1 4 2 74 8 0.8 1 6 2 75 13 0.8 1 9 4 76 10 0.8 1 10 77 8 0.8 1 7 1 78 7 0.8 1 7 79 9 0.8 1 8 1 80 10 0.8 1 9 1 81 4 0.8 1 1 3 82 15 0.8 1 13 2 83 3 0.8 1 3 84 7 0.8 1 5 2 85 15 0.8 1 12 3 86 11 0.8 1 10 1 87 6 0.8 1 6 88 7 0.8 1 6 1 89 8 0.8 1 7 1 90 13 0.8 1 11 2 91 11 0.8 1 8 3 92 12 0.8 1 11 1 93 14 0.8 1 12 2 94 14 0.8 1 12 2 95 14 0.8 1 14 96 14 0.8 1 13 1 97 14 0.8 1 13 1 98 9 0.8 1 8 1 99 10 0.8 1 9 1 100 12 0.8 1 11 1 101 14 0.8 1 12 2 102 11 0.8 1 8 3 103 11 0.8 1 8 3 104 12 0.8 1 9 3 105 12 0.8 1 9 3 106 8 0.8 1 5 3 107 7 0.8 1 6 1 108 15 0.8 1 13 2 109 15 0.8 1 10 5 110 11 0.8 1 10 1 111 12 0.8 1 12 112 12 0.8 1 9 3 113 10 0.8 1 7 3 114 27 0.8 1 21 6 115 13 0.8 1 8 5 116 22 0.8 1 20 2 117 26 0.8 1 21 5 118 15 0.8 1 13 2 119 29 0.8 1 27 2 120 20 0.8 1 19 1 121 20 0.8 1 17 3 122 23 0.8 1 19 4 123 20 0.8 1 17 3 124 21 0.8 1 14 7 125 26 0.8 1 22 4 126 20 0.8 1 16 4 127 25 0.8 1 20 5 128 25 0.8 1 23 2 129 25 0.8 1 23 2 130 26 0.8 1 22 4 131 22 0.8 1 21 1 132 30 0.8 1 27 3 133 35 0.8 1 20 15 134 37 0.8 1 26 11 135 45 0.8 1 21 24 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R1.fq.gz ============================================= 52847841 sequences processed in total