SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_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_10_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1730.29 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 52,847,841 Reads with adapters: 22,781,010 (43.1%) Reads written (passing filters): 52,847,841 (100.0%) Total basepairs processed: 6,661,118,919 bp Quality-trimmed: 2,209,762 bp (0.0%) Total written (filtered): 6,632,042,202 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22781010 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 20322773 13211960.2 0 20322773 2 1590779 3302990.1 0 1590779 3 459662 825747.5 0 459662 4 302784 206436.9 0 302784 5 55915 51609.2 0 55915 6 14196 12902.3 0 14196 7 10464 3225.6 0 10464 8 7831 806.4 0 7831 9 2067 201.6 0 1683 384 10 13009 50.4 1 11893 1116 11 172 12.6 1 26 146 12 53 3.1 1 10 43 13 9 0.8 1 6 3 14 6 0.8 1 5 1 15 7 0.8 1 6 1 16 1 0.8 1 1 17 6 0.8 1 5 1 18 5 0.8 1 4 1 19 11 0.8 1 8 3 20 5 0.8 1 2 3 21 4 0.8 1 2 2 22 7 0.8 1 1 6 23 9 0.8 1 3 6 24 7 0.8 1 2 5 25 2 0.8 1 1 1 26 1 0.8 1 1 27 7 0.8 1 3 4 28 5 0.8 1 3 2 29 7 0.8 1 6 1 30 11 0.8 1 7 4 31 3 0.8 1 3 32 7 0.8 1 2 5 33 10 0.8 1 7 3 34 6 0.8 1 4 2 35 5 0.8 1 2 3 36 7 0.8 1 6 1 37 1 0.8 1 1 38 6 0.8 1 3 3 39 5 0.8 1 3 2 40 9 0.8 1 6 3 41 3 0.8 1 2 1 42 6 0.8 1 5 1 43 4 0.8 1 2 2 44 3 0.8 1 1 2 45 3 0.8 1 1 2 46 6 0.8 1 6 47 5 0.8 1 3 2 48 8 0.8 1 7 1 49 8 0.8 1 4 4 50 7 0.8 1 3 4 51 4 0.8 1 3 1 52 4 0.8 1 4 53 8 0.8 1 5 3 54 7 0.8 1 7 55 6 0.8 1 4 2 56 15 0.8 1 11 4 57 12 0.8 1 8 4 58 6 0.8 1 6 59 4 0.8 1 4 60 12 0.8 1 9 3 61 6 0.8 1 4 2 62 7 0.8 1 7 63 7 0.8 1 4 3 64 11 0.8 1 9 2 65 2 0.8 1 2 66 9 0.8 1 7 2 67 5 0.8 1 5 68 11 0.8 1 8 3 69 3 0.8 1 2 1 70 4 0.8 1 1 3 71 5 0.8 1 4 1 72 5 0.8 1 4 1 73 11 0.8 1 11 74 9 0.8 1 8 1 75 6 0.8 1 6 76 3 0.8 1 3 77 4 0.8 1 4 78 12 0.8 1 9 3 79 9 0.8 1 7 2 80 8 0.8 1 5 3 81 12 0.8 1 11 1 82 1 0.8 1 0 1 83 10 0.8 1 9 1 84 7 0.8 1 4 3 85 8 0.8 1 5 3 86 10 0.8 1 8 2 87 11 0.8 1 11 88 10 0.8 1 10 89 7 0.8 1 7 90 18 0.8 1 17 1 91 9 0.8 1 8 1 92 9 0.8 1 9 93 8 0.8 1 5 3 94 19 0.8 1 18 1 95 9 0.8 1 9 96 8 0.8 1 7 1 97 9 0.8 1 5 4 98 8 0.8 1 7 1 99 12 0.8 1 11 1 100 11 0.8 1 11 101 10 0.8 1 7 3 102 10 0.8 1 7 3 103 9 0.8 1 9 104 11 0.8 1 11 105 4 0.8 1 3 1 106 12 0.8 1 10 2 107 13 0.8 1 12 1 108 27 0.8 1 25 2 109 10 0.8 1 9 1 110 10 0.8 1 10 111 11 0.8 1 10 1 112 15 0.8 1 12 3 113 15 0.8 1 14 1 114 16 0.8 1 14 2 115 17 0.8 1 15 2 116 22 0.8 1 18 4 117 18 0.8 1 16 2 118 21 0.8 1 16 5 119 11 0.8 1 9 2 120 17 0.8 1 16 1 121 27 0.8 1 20 7 122 17 0.8 1 13 4 123 21 0.8 1 18 3 124 20 0.8 1 16 4 125 22 0.8 1 20 2 126 18 0.8 1 15 3 127 25 0.8 1 23 2 128 21 0.8 1 20 1 129 31 0.8 1 24 7 130 25 0.8 1 19 6 131 26 0.8 1 25 1 132 29 0.8 1 22 7 133 32 0.8 1 26 6 134 33 0.8 1 20 13 135 46 0.8 1 17 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R2.fq.gz ============================================= 52847841 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 52847841 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 254964 (0.48%)