SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_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_11_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1820.98 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 57,092,207 Reads with adapters: 24,564,038 (43.0%) Reads written (passing filters): 57,092,207 (100.0%) Total basepairs processed: 7,194,811,854 bp Quality-trimmed: 2,160,013 bp (0.0%) Total written (filtered): 7,163,488,585 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24564038 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21756752 14273051.8 0 21756752 2 1861665 3568262.9 0 1861665 3 507444 892065.7 0 507444 4 321170 223016.4 0 321170 5 62573 55754.1 0 62573 6 16175 13938.5 0 16175 7 11234 3484.6 0 11234 8 8549 871.2 0 8549 9 2068 217.8 0 1619 449 10 14386 54.4 1 13213 1173 11 164 13.6 1 27 137 12 70 3.4 1 15 55 13 10 0.9 1 3 7 14 18 0.9 1 14 4 15 8 0.9 1 5 3 16 16 0.9 1 9 7 17 9 0.9 1 7 2 18 24 0.9 1 11 13 19 24 0.9 1 18 6 20 6 0.9 1 3 3 21 3 0.9 1 3 22 13 0.9 1 5 8 23 9 0.9 1 9 24 20 0.9 1 14 6 25 4 0.9 1 1 3 26 12 0.9 1 9 3 27 9 0.9 1 8 1 28 5 0.9 1 4 1 29 10 0.9 1 7 3 30 15 0.9 1 8 7 31 10 0.9 1 7 3 32 4 0.9 1 2 2 33 14 0.9 1 11 3 34 6 0.9 1 5 1 35 11 0.9 1 10 1 36 6 0.9 1 4 2 37 12 0.9 1 8 4 38 15 0.9 1 11 4 39 8 0.9 1 5 3 40 8 0.9 1 7 1 41 9 0.9 1 4 5 42 20 0.9 1 11 9 43 14 0.9 1 6 8 44 19 0.9 1 14 5 45 3 0.9 1 1 2 46 8 0.9 1 6 2 47 5 0.9 1 4 1 48 16 0.9 1 12 4 49 9 0.9 1 8 1 50 14 0.9 1 10 4 51 6 0.9 1 6 52 13 0.9 1 8 5 53 5 0.9 1 3 2 54 3 0.9 1 2 1 55 15 0.9 1 11 4 56 6 0.9 1 4 2 57 7 0.9 1 7 58 11 0.9 1 9 2 59 7 0.9 1 6 1 60 6 0.9 1 6 61 14 0.9 1 11 3 62 18 0.9 1 11 7 63 7 0.9 1 5 2 64 8 0.9 1 6 2 65 4 0.9 1 3 1 66 10 0.9 1 9 1 67 12 0.9 1 9 3 68 19 0.9 1 16 3 69 11 0.9 1 10 1 70 8 0.9 1 7 1 71 8 0.9 1 7 1 72 14 0.9 1 7 7 73 9 0.9 1 9 74 11 0.9 1 7 4 75 8 0.9 1 7 1 76 14 0.9 1 9 5 77 14 0.9 1 12 2 78 14 0.9 1 12 2 79 11 0.9 1 8 3 80 9 0.9 1 8 1 81 14 0.9 1 14 82 8 0.9 1 7 1 83 20 0.9 1 18 2 84 13 0.9 1 13 85 17 0.9 1 13 4 86 4 0.9 1 4 87 10 0.9 1 8 2 88 18 0.9 1 12 6 89 12 0.9 1 10 2 90 14 0.9 1 12 2 91 13 0.9 1 12 1 92 12 0.9 1 8 4 93 9 0.9 1 7 2 94 12 0.9 1 8 4 95 15 0.9 1 12 3 96 8 0.9 1 6 2 97 12 0.9 1 9 3 98 15 0.9 1 11 4 99 10 0.9 1 8 2 100 13 0.9 1 10 3 101 11 0.9 1 9 2 102 14 0.9 1 13 1 103 10 0.9 1 10 104 18 0.9 1 17 1 105 16 0.9 1 16 106 8 0.9 1 6 2 107 12 0.9 1 11 1 108 23 0.9 1 20 3 109 23 0.9 1 19 4 110 11 0.9 1 10 1 111 19 0.9 1 17 2 112 9 0.9 1 7 2 113 18 0.9 1 13 5 114 22 0.9 1 21 1 115 15 0.9 1 11 4 116 21 0.9 1 18 3 117 22 0.9 1 18 4 118 31 0.9 1 29 2 119 21 0.9 1 17 4 120 32 0.9 1 27 5 121 30 0.9 1 21 9 122 24 0.9 1 23 1 123 29 0.9 1 24 5 124 21 0.9 1 18 3 125 21 0.9 1 18 3 126 27 0.9 1 25 2 127 26 0.9 1 20 6 128 28 0.9 1 22 6 129 20 0.9 1 18 2 130 47 0.9 1 41 6 131 45 0.9 1 35 10 132 31 0.9 1 28 3 133 31 0.9 1 24 7 134 36 0.9 1 22 14 135 39 0.9 1 17 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R1.fq.gz ============================================= 57092207 sequences processed in total