SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_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_18_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1671.85 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 51,977,624 Reads with adapters: 22,212,667 (42.7%) Reads written (passing filters): 51,977,624 (100.0%) Total basepairs processed: 6,536,857,225 bp Quality-trimmed: 1,957,739 bp (0.0%) Total written (filtered): 6,508,713,820 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22212667 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19795170 12994406.0 0 19795170 2 1568340 3248601.5 0 1568340 3 450861 812150.4 0 450861 4 297135 203037.6 0 297135 5 55089 50759.4 0 55089 6 13240 12689.8 0 13240 7 9989 3172.5 0 9989 8 7650 793.1 0 7650 9 2021 198.3 0 1637 384 10 12013 49.6 1 11024 989 11 161 12.4 1 25 136 12 52 3.1 1 9 43 13 3 0.8 1 1 2 14 5 0.8 1 2 3 15 6 0.8 1 3 3 16 1 0.8 1 1 17 7 0.8 1 5 2 18 1 0.8 1 0 1 19 9 0.8 1 3 6 20 8 0.8 1 4 4 21 4 0.8 1 3 1 22 12 0.8 1 7 5 23 3 0.8 1 1 2 24 6 0.8 1 5 1 25 7 0.8 1 4 3 26 6 0.8 1 4 2 27 3 0.8 1 2 1 28 10 0.8 1 8 2 29 5 0.8 1 2 3 30 9 0.8 1 8 1 31 5 0.8 1 5 32 5 0.8 1 4 1 33 5 0.8 1 2 3 34 3 0.8 1 2 1 35 5 0.8 1 2 3 36 1 0.8 1 1 37 1 0.8 1 0 1 38 3 0.8 1 3 39 1 0.8 1 0 1 40 7 0.8 1 7 41 1 0.8 1 1 42 6 0.8 1 3 3 43 2 0.8 1 1 1 44 5 0.8 1 2 3 45 7 0.8 1 5 2 46 8 0.8 1 6 2 47 6 0.8 1 2 4 48 7 0.8 1 4 3 49 6 0.8 1 3 3 50 4 0.8 1 2 2 51 2 0.8 1 2 52 2 0.8 1 1 1 53 8 0.8 1 6 2 54 9 0.8 1 9 55 3 0.8 1 1 2 56 3 0.8 1 2 1 57 6 0.8 1 5 1 58 8 0.8 1 5 3 59 2 0.8 1 2 60 4 0.8 1 3 1 61 1 0.8 1 1 62 4 0.8 1 2 2 63 10 0.8 1 7 3 64 11 0.8 1 9 2 65 3 0.8 1 1 2 66 1 0.8 1 1 67 4 0.8 1 4 68 6 0.8 1 6 69 7 0.8 1 3 4 70 8 0.8 1 8 71 6 0.8 1 6 72 1 0.8 1 1 73 4 0.8 1 3 1 74 4 0.8 1 4 75 6 0.8 1 6 76 5 0.8 1 5 77 5 0.8 1 5 78 3 0.8 1 2 1 79 2 0.8 1 1 1 80 5 0.8 1 4 1 81 8 0.8 1 7 1 82 2 0.8 1 2 83 8 0.8 1 4 4 84 5 0.8 1 3 2 85 5 0.8 1 4 1 86 7 0.8 1 5 2 87 2 0.8 1 2 88 6 0.8 1 6 89 6 0.8 1 5 1 90 5 0.8 1 3 2 91 4 0.8 1 4 92 10 0.8 1 7 3 93 5 0.8 1 5 94 5 0.8 1 1 4 95 6 0.8 1 6 96 8 0.8 1 6 2 97 9 0.8 1 7 2 98 8 0.8 1 6 2 99 8 0.8 1 8 100 4 0.8 1 3 1 101 8 0.8 1 8 102 7 0.8 1 6 1 103 8 0.8 1 6 2 104 8 0.8 1 5 3 105 7 0.8 1 6 1 106 15 0.8 1 15 107 9 0.8 1 8 1 108 7 0.8 1 6 1 109 9 0.8 1 7 2 110 11 0.8 1 9 2 111 14 0.8 1 11 3 112 9 0.8 1 6 3 113 9 0.8 1 6 3 114 14 0.8 1 13 1 115 8 0.8 1 5 3 116 6 0.8 1 6 117 11 0.8 1 9 2 118 14 0.8 1 11 3 119 16 0.8 1 15 1 120 9 0.8 1 6 3 121 19 0.8 1 14 5 122 15 0.8 1 14 1 123 14 0.8 1 11 3 124 12 0.8 1 8 4 125 12 0.8 1 10 2 126 11 0.8 1 10 1 127 20 0.8 1 17 3 128 15 0.8 1 13 2 129 20 0.8 1 17 3 130 19 0.8 1 18 1 131 18 0.8 1 15 3 132 19 0.8 1 14 5 133 21 0.8 1 14 7 134 27 0.8 1 18 9 135 48 0.8 1 19 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R2.fq.gz ============================================= 51977624 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 51977624 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 264448 (0.51%)