SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_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_7_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2765.69 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 82,933,633 Reads with adapters: 36,117,516 (43.5%) Reads written (passing filters): 82,933,633 (100.0%) Total basepairs processed: 10,515,361,816 bp Quality-trimmed: 3,279,955 bp (0.0%) Total written (filtered): 10,469,702,809 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36117516 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.1% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32338767 20733408.2 0 32338767 2 2433358 5183352.1 0 2433358 3 726050 1295838.0 0 726050 4 462161 323959.5 0 462161 5 84776 80989.9 0 84776 6 20704 20247.5 0 20704 7 15079 5061.9 0 15079 8 11270 1265.5 0 11270 9 3227 316.4 0 2607 620 10 19965 79.1 1 18231 1734 11 257 19.8 1 28 229 12 62 4.9 1 14 48 13 20 1.2 1 10 10 14 8 1.2 1 1 7 15 7 1.2 1 4 3 16 4 1.2 1 2 2 17 7 1.2 1 2 5 18 4 1.2 1 3 1 19 8 1.2 1 4 4 20 10 1.2 1 7 3 21 5 1.2 1 3 2 22 11 1.2 1 4 7 23 12 1.2 1 7 5 24 12 1.2 1 7 5 25 3 1.2 1 3 26 11 1.2 1 7 4 27 12 1.2 1 6 6 28 17 1.2 1 9 8 29 5 1.2 1 4 1 30 3 1.2 1 2 1 31 2 1.2 1 1 1 32 8 1.2 1 4 4 33 8 1.2 1 4 4 34 7 1.2 1 6 1 35 8 1.2 1 6 2 36 15 1.2 1 9 6 37 3 1.2 1 1 2 38 7 1.2 1 6 1 39 3 1.2 1 2 1 40 10 1.2 1 6 4 41 8 1.2 1 6 2 42 8 1.2 1 6 2 43 7 1.2 1 6 1 44 7 1.2 1 4 3 45 9 1.2 1 8 1 46 8 1.2 1 6 2 47 5 1.2 1 2 3 48 12 1.2 1 10 2 49 10 1.2 1 7 3 50 13 1.2 1 7 6 51 8 1.2 1 7 1 52 4 1.2 1 3 1 53 8 1.2 1 6 2 54 3 1.2 1 2 1 55 13 1.2 1 11 2 56 4 1.2 1 4 57 11 1.2 1 7 4 58 4 1.2 1 4 59 10 1.2 1 6 4 60 11 1.2 1 8 3 61 5 1.2 1 5 62 9 1.2 1 7 2 63 9 1.2 1 8 1 64 13 1.2 1 12 1 65 6 1.2 1 5 1 66 9 1.2 1 7 2 67 6 1.2 1 6 68 12 1.2 1 12 69 10 1.2 1 7 3 70 20 1.2 1 15 5 71 11 1.2 1 6 5 72 9 1.2 1 7 2 73 14 1.2 1 14 74 10 1.2 1 7 3 75 12 1.2 1 10 2 76 8 1.2 1 7 1 77 11 1.2 1 10 1 78 14 1.2 1 11 3 79 11 1.2 1 10 1 80 10 1.2 1 9 1 81 16 1.2 1 16 82 9 1.2 1 8 1 83 17 1.2 1 13 4 84 17 1.2 1 15 2 85 17 1.2 1 12 5 86 18 1.2 1 14 4 87 11 1.2 1 8 3 88 16 1.2 1 16 89 15 1.2 1 11 4 90 13 1.2 1 13 91 9 1.2 1 6 3 92 10 1.2 1 10 93 13 1.2 1 13 94 17 1.2 1 14 3 95 12 1.2 1 11 1 96 20 1.2 1 16 4 97 18 1.2 1 13 5 98 14 1.2 1 11 3 99 12 1.2 1 9 3 100 16 1.2 1 12 4 101 21 1.2 1 16 5 102 15 1.2 1 12 3 103 13 1.2 1 10 3 104 13 1.2 1 10 3 105 26 1.2 1 23 3 106 12 1.2 1 9 3 107 18 1.2 1 15 3 108 18 1.2 1 12 6 109 18 1.2 1 17 1 110 21 1.2 1 19 2 111 21 1.2 1 19 2 112 19 1.2 1 16 3 113 19 1.2 1 15 4 114 24 1.2 1 20 4 115 12 1.2 1 10 2 116 35 1.2 1 29 6 117 21 1.2 1 17 4 118 17 1.2 1 15 2 119 34 1.2 1 29 5 120 18 1.2 1 15 3 121 20 1.2 1 18 2 122 33 1.2 1 28 5 123 20 1.2 1 16 4 124 21 1.2 1 20 1 125 22 1.2 1 18 4 126 33 1.2 1 28 5 127 45 1.2 1 36 9 128 36 1.2 1 32 4 129 37 1.2 1 28 9 130 43 1.2 1 41 2 131 43 1.2 1 36 7 132 39 1.2 1 34 5 133 47 1.2 1 33 14 134 50 1.2 1 38 12 135 64 1.2 1 35 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R2.fq.gz ============================================= 82933633 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82933633 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 357666 (0.43%)