SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_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_1_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1774.13 s (34 µs/read; 1.77 M reads/minute). === Summary === Total reads processed: 52,225,074 Reads with adapters: 22,305,466 (42.7%) Reads written (passing filters): 52,225,074 (100.0%) Total basepairs processed: 6,552,607,764 bp Quality-trimmed: 2,651,242 bp (0.0%) Total written (filtered): 6,523,511,397 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22305466 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19847833 13056268.5 0 19847833 2 1569666 3264067.1 0 1569666 3 455047 816016.8 0 455047 4 309134 204004.2 0 309134 5 65255 51001.0 0 65255 6 16274 12750.3 0 16274 7 12211 3187.6 0 12211 8 9595 796.9 0 9595 9 2853 199.2 0 2440 413 10 16558 49.8 1 15111 1447 11 195 12.5 1 29 166 12 46 3.1 1 7 39 13 8 0.8 1 1 7 14 6 0.8 1 1 5 15 5 0.8 1 1 4 16 1 0.8 1 0 1 17 8 0.8 1 4 4 18 3 0.8 1 2 1 19 3 0.8 1 1 2 21 4 0.8 1 1 3 23 1 0.8 1 1 24 5 0.8 1 1 4 25 5 0.8 1 1 4 26 1 0.8 1 1 27 1 0.8 1 1 28 2 0.8 1 1 1 29 2 0.8 1 2 30 3 0.8 1 2 1 31 3 0.8 1 1 2 32 6 0.8 1 1 5 33 10 0.8 1 6 4 34 4 0.8 1 0 4 35 3 0.8 1 0 3 36 5 0.8 1 4 1 37 1 0.8 1 1 38 1 0.8 1 1 39 4 0.8 1 3 1 40 4 0.8 1 2 2 42 5 0.8 1 1 4 44 4 0.8 1 2 2 45 3 0.8 1 1 2 46 4 0.8 1 3 1 47 9 0.8 1 4 5 48 2 0.8 1 2 49 2 0.8 1 2 50 3 0.8 1 0 3 51 2 0.8 1 2 52 1 0.8 1 1 53 5 0.8 1 3 2 54 2 0.8 1 1 1 55 2 0.8 1 0 2 56 1 0.8 1 1 57 4 0.8 1 3 1 58 1 0.8 1 1 59 2 0.8 1 1 1 60 8 0.8 1 7 1 61 5 0.8 1 4 1 62 4 0.8 1 2 2 63 7 0.8 1 4 3 64 4 0.8 1 2 2 65 4 0.8 1 2 2 66 5 0.8 1 5 67 2 0.8 1 1 1 68 6 0.8 1 5 1 69 3 0.8 1 3 70 3 0.8 1 2 1 71 2 0.8 1 2 72 6 0.8 1 4 2 73 2 0.8 1 2 74 2 0.8 1 1 1 75 6 0.8 1 4 2 76 2 0.8 1 1 1 77 5 0.8 1 3 2 78 5 0.8 1 3 2 79 2 0.8 1 2 80 2 0.8 1 1 1 81 2 0.8 1 2 82 5 0.8 1 3 2 83 4 0.8 1 2 2 84 2 0.8 1 2 85 4 0.8 1 2 2 86 5 0.8 1 3 2 87 4 0.8 1 4 88 7 0.8 1 7 89 8 0.8 1 8 90 1 0.8 1 0 1 91 6 0.8 1 4 2 92 5 0.8 1 3 2 93 8 0.8 1 8 94 7 0.8 1 7 95 6 0.8 1 4 2 96 2 0.8 1 1 1 97 10 0.8 1 7 3 98 7 0.8 1 6 1 99 8 0.8 1 7 1 100 7 0.8 1 6 1 101 8 0.8 1 5 3 102 5 0.8 1 5 103 9 0.8 1 9 104 8 0.8 1 8 105 5 0.8 1 4 1 106 12 0.8 1 11 1 107 10 0.8 1 8 2 108 16 0.8 1 15 1 109 10 0.8 1 10 110 7 0.8 1 5 2 111 7 0.8 1 6 1 112 11 0.8 1 9 2 113 6 0.8 1 2 4 114 11 0.8 1 9 2 115 7 0.8 1 6 1 116 12 0.8 1 12 117 9 0.8 1 7 2 118 11 0.8 1 7 4 119 18 0.8 1 15 3 120 11 0.8 1 8 3 121 14 0.8 1 14 122 17 0.8 1 14 3 123 11 0.8 1 10 1 124 8 0.8 1 7 1 125 16 0.8 1 14 2 126 15 0.8 1 15 127 15 0.8 1 13 2 128 24 0.8 1 22 2 129 14 0.8 1 13 1 130 15 0.8 1 9 6 131 16 0.8 1 13 3 132 25 0.8 1 19 6 133 14 0.8 1 7 7 134 33 0.8 1 20 13 135 25 0.8 1 11 14 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R2.fq.gz ============================================= 52225074 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 52225074 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 274601 (0.53%)