SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.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_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2655.20 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 82,933,633 Reads with adapters: 36,177,192 (43.6%) Reads written (passing filters): 82,933,633 (100.0%) Total basepairs processed: 10,519,950,530 bp Quality-trimmed: 2,898,401 bp (0.0%) Total written (filtered): 10,474,395,775 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36177192 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.3% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32189614 20733408.2 0 32189614 2 2643851 5183352.1 0 2643851 3 730512 1295838.0 0 730512 4 454107 323959.5 0 454107 5 83925 80989.9 0 83925 6 21891 20247.5 0 21891 7 15266 5061.9 0 15266 8 11574 1265.5 0 11574 9 3140 316.4 0 2517 623 10 20789 79.1 1 19181 1608 11 274 19.8 1 43 231 12 104 4.9 1 32 72 13 11 1.2 1 3 8 14 18 1.2 1 10 8 15 7 1.2 1 4 3 16 21 1.2 1 15 6 17 2 1.2 1 1 1 18 35 1.2 1 24 11 19 53 1.2 1 34 19 20 5 1.2 1 2 3 21 5 1.2 1 3 2 22 10 1.2 1 6 4 23 21 1.2 1 15 6 24 33 1.2 1 19 14 25 7 1.2 1 5 2 26 10 1.2 1 6 4 27 14 1.2 1 10 4 28 4 1.2 1 3 1 29 11 1.2 1 8 3 30 28 1.2 1 22 6 31 20 1.2 1 12 8 32 10 1.2 1 6 4 33 35 1.2 1 22 13 34 12 1.2 1 10 2 35 12 1.2 1 8 4 36 15 1.2 1 10 5 37 16 1.2 1 13 3 38 9 1.2 1 7 2 39 17 1.2 1 12 5 40 12 1.2 1 7 5 41 8 1.2 1 6 2 42 15 1.2 1 8 7 43 19 1.2 1 12 7 44 22 1.2 1 17 5 45 6 1.2 1 6 46 10 1.2 1 6 4 47 5 1.2 1 5 48 26 1.2 1 20 6 49 7 1.2 1 5 2 50 6 1.2 1 3 3 51 17 1.2 1 9 8 52 18 1.2 1 14 4 53 15 1.2 1 13 2 54 6 1.2 1 3 3 55 27 1.2 1 21 6 56 17 1.2 1 10 7 57 8 1.2 1 5 3 58 8 1.2 1 6 2 59 8 1.2 1 6 2 60 6 1.2 1 5 1 61 11 1.2 1 9 2 62 18 1.2 1 15 3 63 6 1.2 1 6 64 11 1.2 1 9 2 65 11 1.2 1 11 66 17 1.2 1 8 9 67 13 1.2 1 9 4 68 7 1.2 1 5 2 69 13 1.2 1 13 70 12 1.2 1 10 2 71 6 1.2 1 6 72 13 1.2 1 10 3 73 18 1.2 1 15 3 74 6 1.2 1 6 75 15 1.2 1 11 4 76 8 1.2 1 7 1 77 10 1.2 1 7 3 78 12 1.2 1 9 3 79 14 1.2 1 12 2 80 9 1.2 1 8 1 81 11 1.2 1 11 82 11 1.2 1 9 2 83 13 1.2 1 11 2 84 12 1.2 1 12 85 7 1.2 1 6 1 86 4 1.2 1 4 87 9 1.2 1 6 3 88 10 1.2 1 8 2 89 13 1.2 1 9 4 90 15 1.2 1 14 1 91 21 1.2 1 18 3 92 13 1.2 1 12 1 93 17 1.2 1 16 1 94 23 1.2 1 21 2 95 10 1.2 1 9 1 96 9 1.2 1 9 97 12 1.2 1 12 98 15 1.2 1 12 3 99 18 1.2 1 16 2 100 13 1.2 1 9 4 101 12 1.2 1 10 2 102 14 1.2 1 12 2 103 15 1.2 1 13 2 104 11 1.2 1 9 2 105 16 1.2 1 13 3 106 12 1.2 1 9 3 107 19 1.2 1 17 2 108 22 1.2 1 19 3 109 23 1.2 1 20 3 110 14 1.2 1 13 1 111 31 1.2 1 24 7 112 16 1.2 1 11 5 113 22 1.2 1 19 3 114 16 1.2 1 13 3 115 20 1.2 1 18 2 116 27 1.2 1 25 2 117 14 1.2 1 13 1 118 27 1.2 1 25 2 119 28 1.2 1 22 6 120 38 1.2 1 35 3 121 22 1.2 1 21 1 122 30 1.2 1 26 4 123 25 1.2 1 23 2 124 26 1.2 1 23 3 125 40 1.2 1 33 7 126 25 1.2 1 23 2 127 25 1.2 1 22 3 128 24 1.2 1 21 3 129 27 1.2 1 23 4 130 47 1.2 1 41 6 131 53 1.2 1 46 7 132 45 1.2 1 38 7 133 67 1.2 1 52 15 134 46 1.2 1 25 21 135 53 1.2 1 30 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.fq.gz ============================================= 82933633 sequences processed in total