SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_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_22_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1627.27 s (34 µs/read; 1.77 M reads/minute). === Summary === Total reads processed: 47,948,800 Reads with adapters: 20,718,810 (43.2%) Reads written (passing filters): 47,948,800 (100.0%) Total basepairs processed: 6,055,877,417 bp Quality-trimmed: 1,943,004 bp (0.0%) Total written (filtered): 6,029,422,572 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20718810 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: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18375993 11987200.0 0 18375993 2 1552544 2996800.0 0 1552544 3 429835 749200.0 0 429835 4 267870 187300.0 0 267870 5 49252 46825.0 0 49252 6 12776 11706.2 0 12776 7 9104 2926.6 0 9104 8 6650 731.6 0 6650 9 1753 182.9 0 1370 383 10 11436 45.7 1 10502 934 11 156 11.4 1 30 126 12 70 2.9 1 31 39 13 10 0.7 1 3 7 14 20 0.7 1 15 5 15 2 0.7 1 1 1 16 32 0.7 1 24 8 17 5 0.7 1 4 1 18 41 0.7 1 20 21 19 44 0.7 1 33 11 20 2 0.7 1 1 1 21 1 0.7 1 0 1 22 6 0.7 1 2 4 23 23 0.7 1 16 7 24 35 0.7 1 21 14 25 1 0.7 1 1 26 14 0.7 1 11 3 27 15 0.7 1 8 7 28 6 0.7 1 2 4 29 10 0.7 1 8 2 30 23 0.7 1 13 10 31 28 0.7 1 20 8 32 9 0.7 1 6 3 33 30 0.7 1 25 5 34 9 0.7 1 8 1 35 9 0.7 1 7 2 36 20 0.7 1 16 4 37 9 0.7 1 9 38 14 0.7 1 10 4 39 9 0.7 1 6 3 40 10 0.7 1 8 2 41 24 0.7 1 18 6 42 12 0.7 1 9 3 43 16 0.7 1 14 2 44 24 0.7 1 19 5 45 3 0.7 1 1 2 46 6 0.7 1 5 1 47 5 0.7 1 2 3 48 20 0.7 1 17 3 49 13 0.7 1 10 3 50 10 0.7 1 9 1 51 4 0.7 1 3 1 52 26 0.7 1 22 4 53 3 0.7 1 3 54 1 0.7 1 1 55 20 0.7 1 17 3 56 24 0.7 1 20 4 57 5 0.7 1 4 1 58 3 0.7 1 3 59 16 0.7 1 14 2 60 1 0.7 1 1 61 4 0.7 1 3 1 62 16 0.7 1 14 2 63 2 0.7 1 2 64 7 0.7 1 5 2 65 6 0.7 1 4 2 66 18 0.7 1 12 6 67 9 0.7 1 4 5 68 7 0.7 1 6 1 69 4 0.7 1 2 2 70 6 0.7 1 6 71 3 0.7 1 3 72 2 0.7 1 2 73 7 0.7 1 5 2 74 4 0.7 1 4 75 9 0.7 1 7 2 76 5 0.7 1 5 77 3 0.7 1 3 78 5 0.7 1 5 79 5 0.7 1 5 80 7 0.7 1 5 2 81 6 0.7 1 3 3 82 5 0.7 1 5 83 10 0.7 1 9 1 85 7 0.7 1 7 86 4 0.7 1 4 87 7 0.7 1 6 1 88 9 0.7 1 7 2 89 9 0.7 1 4 5 90 5 0.7 1 5 91 5 0.7 1 5 92 7 0.7 1 4 3 93 5 0.7 1 4 1 94 5 0.7 1 2 3 95 7 0.7 1 6 1 96 5 0.7 1 1 4 97 10 0.7 1 6 4 98 2 0.7 1 1 1 99 5 0.7 1 4 1 100 4 0.7 1 4 101 10 0.7 1 10 102 9 0.7 1 8 1 103 10 0.7 1 8 2 104 8 0.7 1 8 105 9 0.7 1 6 3 106 3 0.7 1 1 2 107 11 0.7 1 9 2 108 12 0.7 1 12 109 9 0.7 1 8 1 110 7 0.7 1 6 1 111 9 0.7 1 9 112 6 0.7 1 2 4 113 11 0.7 1 8 3 114 4 0.7 1 2 2 115 14 0.7 1 13 1 116 9 0.7 1 8 1 117 11 0.7 1 8 3 118 15 0.7 1 13 2 119 16 0.7 1 15 1 120 17 0.7 1 13 4 121 17 0.7 1 16 1 122 9 0.7 1 6 3 123 6 0.7 1 4 2 124 16 0.7 1 14 2 125 12 0.7 1 9 3 126 20 0.7 1 15 5 127 10 0.7 1 9 1 128 17 0.7 1 17 129 14 0.7 1 12 2 130 18 0.7 1 16 2 131 17 0.7 1 16 1 132 16 0.7 1 14 2 133 23 0.7 1 19 4 134 30 0.7 1 19 11 135 27 0.7 1 10 17 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R1.fq.gz ============================================= 47948800 sequences processed in total