SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_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_13_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1773.29 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 54,135,312 Reads with adapters: 23,601,218 (43.6%) Reads written (passing filters): 54,135,312 (100.0%) Total basepairs processed: 6,875,391,122 bp Quality-trimmed: 1,991,084 bp (0.0%) Total written (filtered): 6,845,788,397 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23601218 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.0% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21164011 13533828.0 0 21164011 2 1571912 3383457.0 0 1571912 3 470038 845864.2 0 470038 4 299695 211466.1 0 299695 5 52176 52866.5 0 52176 6 12427 13216.6 0 12427 7 8880 3304.2 0 8880 8 6830 826.0 0 6830 9 1975 206.5 0 1582 393 10 12006 51.6 1 10968 1038 11 151 12.9 1 14 137 12 29 3.2 1 7 22 13 6 0.8 1 4 2 14 8 0.8 1 6 2 15 4 0.8 1 3 1 16 3 0.8 1 1 2 17 2 0.8 1 1 1 18 3 0.8 1 1 2 19 5 0.8 1 0 5 20 3 0.8 1 2 1 21 6 0.8 1 2 4 22 5 0.8 1 1 4 23 5 0.8 1 3 2 24 8 0.8 1 7 1 25 12 0.8 1 6 6 26 3 0.8 1 2 1 27 3 0.8 1 1 2 28 12 0.8 1 6 6 29 3 0.8 1 1 2 30 3 0.8 1 3 31 3 0.8 1 1 2 32 12 0.8 1 4 8 33 7 0.8 1 5 2 34 3 0.8 1 1 2 35 4 0.8 1 1 3 36 5 0.8 1 4 1 37 6 0.8 1 4 2 38 5 0.8 1 1 4 39 7 0.8 1 6 1 40 5 0.8 1 5 41 6 0.8 1 3 3 42 7 0.8 1 4 3 43 2 0.8 1 2 44 4 0.8 1 2 2 45 6 0.8 1 3 3 46 8 0.8 1 7 1 47 6 0.8 1 3 3 48 5 0.8 1 3 2 49 6 0.8 1 6 50 7 0.8 1 6 1 51 1 0.8 1 1 52 4 0.8 1 3 1 53 6 0.8 1 6 54 2 0.8 1 2 55 1 0.8 1 1 56 2 0.8 1 1 1 57 6 0.8 1 3 3 58 12 0.8 1 9 3 60 6 0.8 1 3 3 61 4 0.8 1 3 1 62 2 0.8 1 2 63 7 0.8 1 5 2 64 4 0.8 1 4 65 4 0.8 1 3 1 66 6 0.8 1 4 2 67 2 0.8 1 2 68 7 0.8 1 5 2 69 5 0.8 1 5 70 5 0.8 1 3 2 71 2 0.8 1 2 72 2 0.8 1 2 73 9 0.8 1 6 3 74 7 0.8 1 5 2 75 3 0.8 1 1 2 76 6 0.8 1 5 1 77 2 0.8 1 2 78 4 0.8 1 3 1 79 9 0.8 1 9 80 4 0.8 1 2 2 81 4 0.8 1 3 1 82 9 0.8 1 5 4 83 9 0.8 1 7 2 84 7 0.8 1 5 2 85 12 0.8 1 8 4 86 7 0.8 1 5 2 87 3 0.8 1 3 88 2 0.8 1 1 1 89 10 0.8 1 9 1 90 5 0.8 1 3 2 91 2 0.8 1 1 1 92 5 0.8 1 5 93 6 0.8 1 6 94 9 0.8 1 7 2 95 5 0.8 1 4 1 96 3 0.8 1 3 97 13 0.8 1 8 5 98 7 0.8 1 5 2 99 8 0.8 1 6 2 100 5 0.8 1 4 1 101 10 0.8 1 8 2 102 9 0.8 1 5 4 103 10 0.8 1 8 2 104 5 0.8 1 2 3 105 8 0.8 1 4 4 106 8 0.8 1 7 1 107 4 0.8 1 4 108 11 0.8 1 8 3 109 13 0.8 1 11 2 110 9 0.8 1 9 111 17 0.8 1 15 2 112 9 0.8 1 9 113 10 0.8 1 8 2 114 16 0.8 1 15 1 115 11 0.8 1 10 1 116 14 0.8 1 12 2 117 11 0.8 1 10 1 118 6 0.8 1 5 1 119 26 0.8 1 20 6 120 16 0.8 1 11 5 121 26 0.8 1 19 7 122 19 0.8 1 19 123 24 0.8 1 19 5 124 20 0.8 1 19 1 125 24 0.8 1 19 5 126 26 0.8 1 22 4 127 25 0.8 1 24 1 128 20 0.8 1 18 2 129 23 0.8 1 17 6 130 23 0.8 1 17 6 131 20 0.8 1 18 2 132 36 0.8 1 28 8 133 29 0.8 1 27 2 134 34 0.8 1 25 9 135 43 0.8 1 27 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R2.fq.gz ============================================= 54135312 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 54135312 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 223746 (0.41%)