SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_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_12_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1515.62 s (32 µs/read; 1.90 M reads/minute). === Summary === Total reads processed: 47,871,006 Reads with adapters: 20,609,022 (43.1%) Reads written (passing filters): 47,871,006 (100.0%) Total basepairs processed: 6,044,965,124 bp Quality-trimmed: 1,661,047 bp (0.0%) Total written (filtered): 6,019,036,550 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20609022 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 5.9% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18389974 11967751.5 0 18389974 2 1462519 2991937.9 0 1462519 3 393984 747984.5 0 393984 4 261257 186996.1 0 261257 5 55110 46749.0 0 55110 6 13822 11687.3 0 13822 7 9340 2921.8 0 9340 8 6830 730.5 0 6830 9 1917 182.6 0 1555 362 10 12674 45.7 1 11706 968 11 132 11.4 1 27 105 12 57 2.9 1 22 35 13 11 0.7 1 4 7 14 26 0.7 1 12 14 15 6 0.7 1 3 3 16 14 0.7 1 10 4 17 6 0.7 1 2 4 18 43 0.7 1 27 16 19 53 0.7 1 38 15 20 5 0.7 1 3 2 21 4 0.7 1 3 1 22 5 0.7 1 1 4 23 19 0.7 1 10 9 24 28 0.7 1 21 7 25 3 0.7 1 3 26 25 0.7 1 18 7 27 11 0.7 1 4 7 28 4 0.7 1 3 1 29 14 0.7 1 8 6 30 26 0.7 1 18 8 31 32 0.7 1 21 11 32 6 0.7 1 2 4 33 26 0.7 1 17 9 34 16 0.7 1 11 5 35 19 0.7 1 18 1 36 24 0.7 1 18 6 37 4 0.7 1 4 38 13 0.7 1 9 4 39 10 0.7 1 8 2 40 12 0.7 1 5 7 41 16 0.7 1 13 3 42 13 0.7 1 9 4 43 12 0.7 1 9 3 44 14 0.7 1 11 3 45 4 0.7 1 2 2 46 11 0.7 1 6 5 47 2 0.7 1 1 1 48 22 0.7 1 14 8 49 14 0.7 1 12 2 50 2 0.7 1 0 2 51 11 0.7 1 9 2 52 15 0.7 1 11 4 53 5 0.7 1 3 2 54 7 0.7 1 6 1 55 22 0.7 1 15 7 56 17 0.7 1 12 5 57 5 0.7 1 2 3 58 9 0.7 1 7 2 59 14 0.7 1 11 3 60 5 0.7 1 4 1 61 3 0.7 1 2 1 62 11 0.7 1 9 2 63 4 0.7 1 2 2 64 4 0.7 1 3 1 65 5 0.7 1 4 1 66 8 0.7 1 6 2 67 7 0.7 1 7 68 8 0.7 1 7 1 69 4 0.7 1 2 2 70 4 0.7 1 4 71 5 0.7 1 5 72 8 0.7 1 8 73 2 0.7 1 2 74 3 0.7 1 2 1 75 6 0.7 1 3 3 76 7 0.7 1 6 1 77 6 0.7 1 3 3 78 2 0.7 1 1 1 79 2 0.7 1 1 1 80 7 0.7 1 6 1 81 10 0.7 1 8 2 82 6 0.7 1 5 1 83 7 0.7 1 6 1 84 4 0.7 1 4 85 10 0.7 1 8 2 86 11 0.7 1 10 1 87 5 0.7 1 5 88 6 0.7 1 5 1 89 4 0.7 1 3 1 90 5 0.7 1 3 2 91 8 0.7 1 7 1 92 6 0.7 1 5 1 93 9 0.7 1 9 94 4 0.7 1 3 1 95 6 0.7 1 4 2 96 8 0.7 1 8 97 5 0.7 1 5 98 3 0.7 1 3 99 9 0.7 1 7 2 100 9 0.7 1 8 1 101 10 0.7 1 8 2 102 13 0.7 1 9 4 103 10 0.7 1 9 1 104 10 0.7 1 10 105 9 0.7 1 9 106 7 0.7 1 6 1 107 7 0.7 1 5 2 108 3 0.7 1 1 2 109 12 0.7 1 8 4 110 8 0.7 1 8 111 8 0.7 1 8 112 10 0.7 1 7 3 113 9 0.7 1 9 114 8 0.7 1 7 1 115 10 0.7 1 7 3 116 11 0.7 1 8 3 117 10 0.7 1 8 2 118 16 0.7 1 10 6 119 21 0.7 1 18 3 120 15 0.7 1 15 121 16 0.7 1 13 3 122 13 0.7 1 12 1 123 18 0.7 1 18 124 12 0.7 1 11 1 125 9 0.7 1 7 2 126 19 0.7 1 18 1 127 15 0.7 1 14 1 128 20 0.7 1 19 1 129 25 0.7 1 23 2 130 20 0.7 1 19 1 131 18 0.7 1 17 1 132 21 0.7 1 19 2 133 23 0.7 1 17 6 134 18 0.7 1 15 3 135 26 0.7 1 10 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R1.fq.gz ============================================= 47871006 sequences processed in total