SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_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_6_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1752.19 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 54,279,403 Reads with adapters: 23,503,336 (43.3%) Reads written (passing filters): 54,279,403 (100.0%) Total basepairs processed: 6,866,266,970 bp Quality-trimmed: 2,331,881 bp (0.0%) Total written (filtered): 6,836,138,023 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23503336 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 20859514 13569850.8 0 20859514 2 1750993 3392462.7 0 1750993 3 487441 848115.7 0 487441 4 299944 212028.9 0 299944 5 55176 53007.2 0 55176 6 14518 13251.8 0 14518 7 10342 3313.0 0 10342 8 7594 828.2 0 7594 9 2061 207.1 0 1612 449 10 14212 51.8 1 13087 1125 11 164 12.9 1 37 127 12 66 3.2 1 24 42 13 6 0.8 1 1 5 14 13 0.8 1 7 6 15 4 0.8 1 3 1 16 11 0.8 1 7 4 18 32 0.8 1 17 15 19 26 0.8 1 18 8 20 8 0.8 1 5 3 21 6 0.8 1 5 1 22 1 0.8 1 0 1 23 11 0.8 1 7 4 24 18 0.8 1 13 5 25 1 0.8 1 0 1 26 8 0.8 1 5 3 27 7 0.8 1 5 2 28 4 0.8 1 3 1 29 5 0.8 1 2 3 30 14 0.8 1 9 5 31 15 0.8 1 11 4 32 3 0.8 1 3 33 17 0.8 1 12 5 34 4 0.8 1 1 3 35 7 0.8 1 4 3 36 5 0.8 1 5 37 8 0.8 1 2 6 38 6 0.8 1 3 3 39 5 0.8 1 3 2 40 10 0.8 1 9 1 41 7 0.8 1 2 5 42 11 0.8 1 5 6 43 11 0.8 1 8 3 44 7 0.8 1 5 2 45 4 0.8 1 2 2 46 4 0.8 1 4 47 4 0.8 1 3 1 48 10 0.8 1 5 5 49 8 0.8 1 6 2 50 4 0.8 1 3 1 51 4 0.8 1 3 1 52 11 0.8 1 6 5 53 8 0.8 1 6 2 54 6 0.8 1 6 55 14 0.8 1 8 6 56 15 0.8 1 11 4 57 8 0.8 1 4 4 58 2 0.8 1 2 59 4 0.8 1 4 60 2 0.8 1 1 1 61 3 0.8 1 3 62 12 0.8 1 9 3 63 3 0.8 1 3 64 3 0.8 1 3 65 10 0.8 1 8 2 66 9 0.8 1 7 2 67 2 0.8 1 2 68 8 0.8 1 6 2 69 5 0.8 1 2 3 70 5 0.8 1 4 1 71 3 0.8 1 3 72 9 0.8 1 8 1 73 3 0.8 1 3 74 5 0.8 1 2 3 75 6 0.8 1 6 76 10 0.8 1 8 2 77 4 0.8 1 3 1 78 9 0.8 1 7 2 79 6 0.8 1 5 1 80 5 0.8 1 4 1 81 9 0.8 1 9 82 5 0.8 1 4 1 83 8 0.8 1 4 4 84 7 0.8 1 6 1 85 8 0.8 1 7 1 86 9 0.8 1 9 87 8 0.8 1 7 1 88 9 0.8 1 8 1 89 4 0.8 1 4 90 9 0.8 1 8 1 91 12 0.8 1 8 4 92 6 0.8 1 6 93 6 0.8 1 4 2 94 8 0.8 1 5 3 95 7 0.8 1 5 2 96 10 0.8 1 7 3 97 11 0.8 1 5 6 98 6 0.8 1 5 1 99 8 0.8 1 7 1 100 10 0.8 1 8 2 101 8 0.8 1 6 2 102 5 0.8 1 5 103 8 0.8 1 7 1 104 8 0.8 1 6 2 105 10 0.8 1 8 2 106 14 0.8 1 12 2 107 12 0.8 1 10 2 108 19 0.8 1 13 6 109 11 0.8 1 8 3 110 8 0.8 1 5 3 111 9 0.8 1 7 2 112 14 0.8 1 13 1 113 15 0.8 1 13 2 114 16 0.8 1 14 2 115 9 0.8 1 8 1 116 7 0.8 1 7 117 17 0.8 1 15 2 118 9 0.8 1 9 119 11 0.8 1 9 2 120 23 0.8 1 21 2 121 25 0.8 1 25 122 20 0.8 1 17 3 123 23 0.8 1 19 4 124 19 0.8 1 18 1 125 25 0.8 1 22 3 126 18 0.8 1 16 2 127 17 0.8 1 14 3 128 33 0.8 1 30 3 129 26 0.8 1 25 1 130 23 0.8 1 20 3 131 26 0.8 1 20 6 132 29 0.8 1 23 6 133 34 0.8 1 26 8 134 39 0.8 1 29 10 135 42 0.8 1 19 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R1.fq.gz ============================================= 54279403 sequences processed in total