SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_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_18_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1650.50 s (32 µs/read; 1.89 M reads/minute). === Summary === Total reads processed: 51,977,624 Reads with adapters: 22,254,918 (42.8%) Reads written (passing filters): 51,977,624 (100.0%) Total basepairs processed: 6,538,749,697 bp Quality-trimmed: 1,953,148 bp (0.0%) Total written (filtered): 6,510,376,573 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22254918 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 19679963 12994406.0 0 19679963 2 1715586 3248601.5 0 1715586 3 462343 812150.4 0 462343 4 293120 203037.6 0 293120 5 55471 50759.4 0 55471 6 14322 12689.8 0 14322 7 10221 3172.5 0 10221 8 7505 793.1 0 7505 9 1871 198.3 0 1431 440 10 12785 49.6 1 11769 1016 11 155 12.4 1 38 117 12 86 3.1 1 37 49 13 7 0.8 1 0 7 14 32 0.8 1 25 7 15 3 0.8 1 3 16 31 0.8 1 25 6 17 1 0.8 1 0 1 18 38 0.8 1 25 13 19 50 0.8 1 34 16 20 9 0.8 1 7 2 21 1 0.8 1 1 22 5 0.8 1 2 3 23 13 0.8 1 5 8 24 51 0.8 1 39 12 25 4 0.8 1 4 26 21 0.8 1 15 6 27 14 0.8 1 10 4 28 5 0.8 1 5 29 13 0.8 1 7 6 30 26 0.8 1 22 4 31 24 0.8 1 14 10 32 4 0.8 1 2 2 33 25 0.8 1 19 6 34 9 0.8 1 6 3 35 11 0.8 1 6 5 36 20 0.8 1 15 5 37 17 0.8 1 12 5 38 13 0.8 1 11 2 39 6 0.8 1 3 3 40 11 0.8 1 3 8 41 19 0.8 1 15 4 42 18 0.8 1 11 7 43 18 0.8 1 15 3 44 18 0.8 1 14 4 45 7 0.8 1 6 1 46 9 0.8 1 9 47 3 0.8 1 2 1 48 22 0.8 1 13 9 49 14 0.8 1 12 2 50 8 0.8 1 7 1 51 12 0.8 1 6 6 52 17 0.8 1 15 2 53 9 0.8 1 8 1 54 3 0.8 1 1 2 55 30 0.8 1 22 8 56 20 0.8 1 17 3 57 3 0.8 1 3 58 6 0.8 1 4 2 59 11 0.8 1 10 1 60 6 0.8 1 5 1 61 6 0.8 1 4 2 62 15 0.8 1 10 5 63 3 0.8 1 2 1 64 2 0.8 1 1 1 65 3 0.8 1 1 2 66 15 0.8 1 11 4 67 12 0.8 1 11 1 68 4 0.8 1 2 2 69 3 0.8 1 1 2 70 4 0.8 1 4 71 5 0.8 1 4 1 72 7 0.8 1 6 1 73 5 0.8 1 4 1 74 10 0.8 1 7 3 75 5 0.8 1 1 4 76 6 0.8 1 5 1 77 5 0.8 1 5 78 7 0.8 1 4 3 79 5 0.8 1 5 80 9 0.8 1 8 1 81 8 0.8 1 5 3 82 6 0.8 1 4 2 83 9 0.8 1 8 1 84 5 0.8 1 3 2 85 7 0.8 1 5 2 86 5 0.8 1 3 2 87 6 0.8 1 5 1 88 8 0.8 1 7 1 89 10 0.8 1 8 2 90 9 0.8 1 9 91 6 0.8 1 6 92 8 0.8 1 6 2 93 2 0.8 1 2 94 8 0.8 1 7 1 95 8 0.8 1 7 1 96 12 0.8 1 10 2 97 9 0.8 1 8 1 98 4 0.8 1 4 99 8 0.8 1 6 2 100 9 0.8 1 7 2 101 3 0.8 1 2 1 102 14 0.8 1 12 2 103 10 0.8 1 7 3 104 11 0.8 1 9 2 105 3 0.8 1 3 106 11 0.8 1 7 4 107 10 0.8 1 6 4 108 7 0.8 1 7 109 7 0.8 1 7 110 8 0.8 1 5 3 111 6 0.8 1 6 112 9 0.8 1 8 1 113 13 0.8 1 9 4 114 17 0.8 1 15 2 115 15 0.8 1 13 2 116 12 0.8 1 11 1 117 9 0.8 1 5 4 118 17 0.8 1 15 2 119 23 0.8 1 18 5 120 11 0.8 1 9 2 121 10 0.8 1 10 122 22 0.8 1 17 5 123 10 0.8 1 10 124 10 0.8 1 9 1 125 14 0.8 1 14 126 19 0.8 1 16 3 127 18 0.8 1 18 128 27 0.8 1 22 5 129 16 0.8 1 15 1 130 19 0.8 1 16 3 131 19 0.8 1 14 5 132 17 0.8 1 17 133 22 0.8 1 20 2 134 26 0.8 1 19 7 135 30 0.8 1 14 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R1.fq.gz ============================================= 51977624 sequences processed in total