SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_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_3_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1288.01 s (33 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 39,620,531 Reads with adapters: 17,252,677 (43.5%) Reads written (passing filters): 39,620,531 (100.0%) Total basepairs processed: 5,016,985,237 bp Quality-trimmed: 1,682,604 bp (0.0%) Total written (filtered): 4,994,929,003 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17252677 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.5% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15338331 9905132.8 0 15338331 2 1270264 2476283.2 0 1270264 3 353363 619070.8 0 353363 4 216308 154767.7 0 216308 5 38896 38691.9 0 38896 6 10066 9673.0 0 10066 7 7187 2418.2 0 7187 8 5428 604.6 0 5428 9 1518 151.1 0 1212 306 10 9745 37.8 1 8989 756 11 140 9.4 1 34 106 12 77 2.4 1 29 48 13 13 0.6 1 2 11 14 12 0.6 1 7 5 15 5 0.6 1 3 2 16 15 0.6 1 9 6 17 1 0.6 1 1 18 29 0.6 1 21 8 19 31 0.6 1 22 9 20 4 0.6 1 1 3 21 5 0.6 1 2 3 22 7 0.6 1 4 3 23 22 0.6 1 13 9 24 24 0.6 1 16 8 26 15 0.6 1 10 5 27 12 0.6 1 10 2 28 1 0.6 1 1 29 8 0.6 1 3 5 30 19 0.6 1 13 6 31 21 0.6 1 16 5 32 2 0.6 1 2 33 14 0.6 1 9 5 34 5 0.6 1 3 2 35 13 0.6 1 11 2 36 11 0.6 1 8 3 37 11 0.6 1 4 7 38 8 0.6 1 6 2 39 12 0.6 1 10 2 40 11 0.6 1 9 2 41 13 0.6 1 8 5 42 8 0.6 1 8 43 15 0.6 1 9 6 44 10 0.6 1 9 1 45 5 0.6 1 4 1 46 9 0.6 1 7 2 47 5 0.6 1 3 2 48 12 0.6 1 9 3 49 13 0.6 1 10 3 50 6 0.6 1 4 2 51 8 0.6 1 6 2 52 17 0.6 1 13 4 53 11 0.6 1 10 1 54 6 0.6 1 4 2 55 15 0.6 1 10 5 56 15 0.6 1 13 2 57 4 0.6 1 3 1 58 10 0.6 1 8 2 59 10 0.6 1 7 3 60 4 0.6 1 4 61 1 0.6 1 1 62 8 0.6 1 7 1 63 8 0.6 1 7 1 64 4 0.6 1 3 1 65 7 0.6 1 4 3 66 12 0.6 1 8 4 67 8 0.6 1 7 1 68 4 0.6 1 3 1 69 2 0.6 1 1 1 70 3 0.6 1 2 1 71 12 0.6 1 12 72 2 0.6 1 2 73 10 0.6 1 9 1 74 6 0.6 1 3 3 75 9 0.6 1 6 3 76 6 0.6 1 5 1 77 5 0.6 1 5 78 9 0.6 1 7 2 79 11 0.6 1 11 80 7 0.6 1 6 1 81 8 0.6 1 8 82 7 0.6 1 4 3 83 5 0.6 1 3 2 84 11 0.6 1 10 1 85 10 0.6 1 7 3 86 9 0.6 1 8 1 87 8 0.6 1 6 2 88 6 0.6 1 4 2 89 7 0.6 1 7 90 5 0.6 1 4 1 91 12 0.6 1 11 1 92 7 0.6 1 7 93 11 0.6 1 11 94 11 0.6 1 8 3 95 9 0.6 1 8 1 96 7 0.6 1 4 3 97 7 0.6 1 6 1 98 8 0.6 1 7 1 99 7 0.6 1 7 100 8 0.6 1 8 101 9 0.6 1 8 1 102 10 0.6 1 8 2 103 13 0.6 1 9 4 104 9 0.6 1 8 1 105 9 0.6 1 5 4 106 12 0.6 1 12 107 6 0.6 1 6 108 14 0.6 1 12 2 109 8 0.6 1 7 1 110 11 0.6 1 10 1 111 8 0.6 1 7 1 112 14 0.6 1 14 113 10 0.6 1 10 114 6 0.6 1 5 1 115 12 0.6 1 9 3 116 6 0.6 1 5 1 117 15 0.6 1 13 2 118 10 0.6 1 9 1 119 14 0.6 1 12 2 120 17 0.6 1 17 121 14 0.6 1 13 1 122 14 0.6 1 8 6 123 15 0.6 1 13 2 124 13 0.6 1 13 125 9 0.6 1 5 4 126 26 0.6 1 23 3 127 14 0.6 1 11 3 128 30 0.6 1 30 129 29 0.6 1 28 1 130 26 0.6 1 23 3 131 21 0.6 1 19 2 132 26 0.6 1 19 7 133 20 0.6 1 19 1 134 21 0.6 1 11 10 135 39 0.6 1 16 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R1.fq.gz ============================================= 39620531 sequences processed in total