SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_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_8_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1447.08 s (34 µs/read; 1.79 M reads/minute). === Summary === Total reads processed: 43,149,301 Reads with adapters: 18,631,147 (43.2%) Reads written (passing filters): 43,149,301 (100.0%) Total basepairs processed: 5,443,153,167 bp Quality-trimmed: 1,812,726 bp (0.0%) Total written (filtered): 5,419,360,965 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18631147 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: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16618768 10787325.2 0 16618768 2 1296734 2696831.3 0 1296734 3 379833 674207.8 0 379833 4 245864 168552.0 0 245864 5 48781 42138.0 0 48781 6 11644 10534.5 0 11644 7 8534 2633.6 0 8534 8 6628 658.4 0 6628 9 1831 164.6 0 1474 357 10 11430 41.2 1 10505 925 11 149 10.3 1 20 129 12 42 2.6 1 11 31 13 14 0.6 1 3 11 14 3 0.6 1 1 2 15 7 0.6 1 3 4 16 1 0.6 1 1 17 4 0.6 1 1 3 19 3 0.6 1 3 20 1 0.6 1 0 1 21 4 0.6 1 3 1 22 3 0.6 1 1 2 23 6 0.6 1 2 4 24 6 0.6 1 2 4 25 3 0.6 1 1 2 26 7 0.6 1 4 3 27 2 0.6 1 0 2 28 4 0.6 1 3 1 29 3 0.6 1 1 2 30 3 0.6 1 3 31 3 0.6 1 2 1 32 4 0.6 1 2 2 33 2 0.6 1 2 34 2 0.6 1 1 1 35 6 0.6 1 3 3 36 4 0.6 1 2 2 37 2 0.6 1 2 38 1 0.6 1 1 39 5 0.6 1 4 1 40 5 0.6 1 4 1 41 5 0.6 1 4 1 42 7 0.6 1 5 2 43 7 0.6 1 5 2 44 7 0.6 1 2 5 45 3 0.6 1 2 1 46 2 0.6 1 2 47 9 0.6 1 5 4 48 5 0.6 1 3 2 49 5 0.6 1 3 2 50 2 0.6 1 2 51 3 0.6 1 1 2 52 8 0.6 1 6 2 53 5 0.6 1 4 1 54 5 0.6 1 3 2 55 3 0.6 1 3 56 6 0.6 1 5 1 57 10 0.6 1 9 1 58 5 0.6 1 3 2 59 6 0.6 1 6 60 9 0.6 1 7 2 61 3 0.6 1 3 62 1 0.6 1 1 63 3 0.6 1 3 64 4 0.6 1 2 2 65 4 0.6 1 2 2 66 7 0.6 1 4 3 67 2 0.6 1 2 68 4 0.6 1 4 69 6 0.6 1 4 2 70 4 0.6 1 4 72 1 0.6 1 0 1 73 4 0.6 1 3 1 74 1 0.6 1 1 75 6 0.6 1 6 76 7 0.6 1 7 77 5 0.6 1 5 78 5 0.6 1 3 2 79 7 0.6 1 7 80 3 0.6 1 3 81 10 0.6 1 4 6 83 5 0.6 1 5 84 10 0.6 1 8 2 85 5 0.6 1 5 86 6 0.6 1 2 4 87 5 0.6 1 5 88 10 0.6 1 9 1 89 3 0.6 1 2 1 90 4 0.6 1 3 1 91 6 0.6 1 4 2 92 2 0.6 1 2 93 8 0.6 1 8 94 4 0.6 1 3 1 95 4 0.6 1 3 1 96 3 0.6 1 3 97 7 0.6 1 3 4 98 17 0.6 1 13 4 99 13 0.6 1 10 3 100 6 0.6 1 6 101 8 0.6 1 6 2 102 9 0.6 1 6 3 103 4 0.6 1 4 104 6 0.6 1 5 1 105 5 0.6 1 3 2 106 13 0.6 1 11 2 107 7 0.6 1 7 108 6 0.6 1 5 1 109 9 0.6 1 8 1 110 3 0.6 1 3 111 7 0.6 1 5 2 112 12 0.6 1 11 1 113 10 0.6 1 9 1 114 12 0.6 1 8 4 115 8 0.6 1 8 116 14 0.6 1 12 2 117 18 0.6 1 18 118 18 0.6 1 16 2 119 16 0.6 1 15 1 120 15 0.6 1 11 4 121 13 0.6 1 13 122 13 0.6 1 10 3 123 11 0.6 1 10 1 124 13 0.6 1 11 2 125 14 0.6 1 12 2 126 15 0.6 1 10 5 127 16 0.6 1 11 5 128 14 0.6 1 13 1 129 24 0.6 1 22 2 130 18 0.6 1 14 4 131 22 0.6 1 18 4 132 31 0.6 1 23 8 133 25 0.6 1 16 9 134 24 0.6 1 17 7 135 31 0.6 1 10 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R2.fq.gz ============================================= 43149301 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 43149301 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 205242 (0.48%)