SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_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_4_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1715.97 s (34 µs/read; 1.76 M reads/minute). === Summary === Total reads processed: 50,228,886 Reads with adapters: 21,861,473 (43.5%) Reads written (passing filters): 50,228,886 (100.0%) Total basepairs processed: 6,355,763,675 bp Quality-trimmed: 2,416,042 bp (0.0%) Total written (filtered): 6,327,528,676 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21861473 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.5% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19428633 12557221.5 0 19428633 2 1609452 3139305.4 0 1609452 3 451732 784826.3 0 451732 4 273944 196206.6 0 273944 5 51805 49051.6 0 51805 6 13271 12262.9 0 13271 7 9186 3065.7 0 9186 8 6912 766.4 0 6912 9 2001 191.6 0 1610 391 10 12888 47.9 1 11793 1095 11 152 12.0 1 32 120 12 70 3.0 1 24 46 13 15 0.7 1 3 12 14 25 0.7 1 17 8 15 5 0.7 1 3 2 16 13 0.7 1 10 3 17 3 0.7 1 2 1 18 36 0.7 1 22 14 19 26 0.7 1 16 10 20 5 0.7 1 5 21 2 0.7 1 2 22 9 0.7 1 5 4 23 20 0.7 1 12 8 24 23 0.7 1 12 11 25 3 0.7 1 0 3 26 16 0.7 1 13 3 27 17 0.7 1 12 5 28 9 0.7 1 7 2 29 3 0.7 1 3 30 22 0.7 1 9 13 31 24 0.7 1 14 10 32 2 0.7 1 1 1 33 10 0.7 1 9 1 34 5 0.7 1 3 2 35 6 0.7 1 2 4 36 15 0.7 1 15 37 12 0.7 1 8 4 38 13 0.7 1 10 3 39 8 0.7 1 6 2 40 16 0.7 1 12 4 41 13 0.7 1 10 3 42 17 0.7 1 15 2 43 15 0.7 1 12 3 44 15 0.7 1 8 7 45 4 0.7 1 3 1 46 7 0.7 1 5 2 47 1 0.7 1 1 48 16 0.7 1 9 7 49 3 0.7 1 2 1 50 4 0.7 1 4 51 9 0.7 1 6 3 52 16 0.7 1 13 3 53 10 0.7 1 6 4 54 3 0.7 1 0 3 55 13 0.7 1 10 3 56 16 0.7 1 15 1 57 5 0.7 1 4 1 58 7 0.7 1 5 2 59 14 0.7 1 12 2 60 2 0.7 1 0 2 61 5 0.7 1 3 2 62 10 0.7 1 8 2 63 3 0.7 1 2 1 64 7 0.7 1 6 1 65 8 0.7 1 6 2 66 13 0.7 1 10 3 67 9 0.7 1 6 3 68 3 0.7 1 3 69 6 0.7 1 5 1 70 9 0.7 1 6 3 71 4 0.7 1 3 1 72 6 0.7 1 4 2 73 2 0.7 1 2 74 12 0.7 1 8 4 75 9 0.7 1 8 1 76 6 0.7 1 4 2 77 4 0.7 1 3 1 78 7 0.7 1 4 3 79 4 0.7 1 2 2 80 19 0.7 1 16 3 81 11 0.7 1 6 5 82 7 0.7 1 7 83 8 0.7 1 8 84 10 0.7 1 7 3 85 7 0.7 1 7 86 6 0.7 1 6 87 9 0.7 1 8 1 88 5 0.7 1 5 89 4 0.7 1 4 90 10 0.7 1 7 3 91 10 0.7 1 9 1 92 9 0.7 1 9 93 11 0.7 1 10 1 94 7 0.7 1 6 1 95 7 0.7 1 5 2 96 11 0.7 1 6 5 97 5 0.7 1 2 3 98 6 0.7 1 5 1 99 8 0.7 1 8 100 4 0.7 1 3 1 101 10 0.7 1 9 1 102 10 0.7 1 9 1 103 4 0.7 1 3 1 104 11 0.7 1 7 4 105 13 0.7 1 13 106 9 0.7 1 8 1 107 12 0.7 1 10 2 108 10 0.7 1 9 1 109 12 0.7 1 8 4 110 13 0.7 1 12 1 111 10 0.7 1 7 3 112 7 0.7 1 7 113 12 0.7 1 12 114 13 0.7 1 11 2 115 13 0.7 1 10 3 116 15 0.7 1 12 3 117 18 0.7 1 16 2 118 13 0.7 1 11 2 119 18 0.7 1 16 2 120 13 0.7 1 9 4 121 19 0.7 1 16 3 122 14 0.7 1 12 2 123 18 0.7 1 13 5 124 19 0.7 1 17 2 125 18 0.7 1 14 4 126 25 0.7 1 22 3 127 19 0.7 1 18 1 128 19 0.7 1 16 3 129 26 0.7 1 23 3 130 24 0.7 1 19 5 131 19 0.7 1 18 1 132 26 0.7 1 21 5 133 21 0.7 1 18 3 134 21 0.7 1 17 4 135 49 0.7 1 19 30 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R1.fq.gz ============================================= 50228886 sequences processed in total