SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_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_23_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1279.27 s (31 µs/read; 1.91 M reads/minute). === Summary === Total reads processed: 40,743,756 Reads with adapters: 17,444,950 (42.8%) Reads written (passing filters): 40,743,756 (100.0%) Total basepairs processed: 5,122,390,542 bp Quality-trimmed: 1,745,274 bp (0.0%) Total written (filtered): 5,099,945,615 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17444950 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% 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 15432601 10185939.0 0 15432601 2 1339323 2546484.8 0 1339323 3 361842 636621.2 0 361842 4 229699 159155.3 0 229699 5 43790 39788.8 0 43790 6 11029 9947.2 0 11029 7 8042 2486.8 0 8042 8 5919 621.7 0 5919 9 1553 155.4 0 1177 376 10 10046 38.9 1 9143 903 11 134 9.7 1 21 113 12 41 2.4 1 18 23 13 6 0.6 1 0 6 14 11 0.6 1 5 6 15 2 0.6 1 2 16 9 0.6 1 7 2 17 3 0.6 1 2 1 18 18 0.6 1 11 7 19 14 0.6 1 9 5 20 4 0.6 1 2 2 21 2 0.6 1 1 1 22 3 0.6 1 2 1 23 14 0.6 1 8 6 24 11 0.6 1 5 6 25 3 0.6 1 3 26 3 0.6 1 3 27 4 0.6 1 3 1 28 3 0.6 1 1 2 29 5 0.6 1 4 1 30 6 0.6 1 1 5 31 11 0.6 1 8 3 32 2 0.6 1 2 33 12 0.6 1 8 4 34 4 0.6 1 2 2 35 8 0.6 1 8 36 16 0.6 1 13 3 37 4 0.6 1 3 1 38 2 0.6 1 2 39 5 0.6 1 5 40 2 0.6 1 1 1 41 6 0.6 1 5 1 42 6 0.6 1 5 1 43 12 0.6 1 7 5 44 3 0.6 1 3 45 5 0.6 1 4 1 46 6 0.6 1 4 2 47 6 0.6 1 4 2 48 10 0.6 1 9 1 49 3 0.6 1 1 2 50 8 0.6 1 6 2 51 5 0.6 1 3 2 52 8 0.6 1 5 3 53 5 0.6 1 5 54 2 0.6 1 2 55 6 0.6 1 4 2 56 5 0.6 1 1 4 57 5 0.6 1 5 58 4 0.6 1 4 59 4 0.6 1 2 2 60 3 0.6 1 2 1 61 1 0.6 1 1 62 2 0.6 1 2 63 2 0.6 1 1 1 64 4 0.6 1 4 65 3 0.6 1 3 66 10 0.6 1 9 1 67 6 0.6 1 5 1 68 2 0.6 1 2 69 10 0.6 1 8 2 70 2 0.6 1 2 71 2 0.6 1 0 2 72 5 0.6 1 4 1 73 10 0.6 1 8 2 74 6 0.6 1 2 4 75 2 0.6 1 0 2 76 7 0.6 1 2 5 77 7 0.6 1 4 3 78 7 0.6 1 6 1 79 4 0.6 1 4 80 5 0.6 1 4 1 81 8 0.6 1 5 3 82 5 0.6 1 4 1 83 4 0.6 1 3 1 84 8 0.6 1 7 1 85 2 0.6 1 2 86 7 0.6 1 6 1 87 4 0.6 1 2 2 88 6 0.6 1 5 1 89 2 0.6 1 2 90 7 0.6 1 7 91 5 0.6 1 5 92 7 0.6 1 6 1 93 4 0.6 1 4 94 1 0.6 1 1 95 8 0.6 1 7 1 96 4 0.6 1 2 2 97 5 0.6 1 4 1 98 5 0.6 1 3 2 99 9 0.6 1 8 1 100 1 0.6 1 1 101 5 0.6 1 4 1 102 6 0.6 1 5 1 103 8 0.6 1 5 3 104 9 0.6 1 7 2 105 6 0.6 1 6 106 11 0.6 1 8 3 107 5 0.6 1 5 108 10 0.6 1 8 2 109 8 0.6 1 8 110 8 0.6 1 6 2 111 11 0.6 1 8 3 112 6 0.6 1 6 113 19 0.6 1 18 1 114 10 0.6 1 6 4 115 12 0.6 1 10 2 116 9 0.6 1 8 1 117 10 0.6 1 9 1 118 13 0.6 1 9 4 119 12 0.6 1 11 1 120 23 0.6 1 18 5 121 15 0.6 1 14 1 122 8 0.6 1 8 123 16 0.6 1 15 1 124 8 0.6 1 6 2 125 15 0.6 1 13 2 126 11 0.6 1 11 127 12 0.6 1 10 2 128 11 0.6 1 11 129 25 0.6 1 22 3 130 20 0.6 1 19 1 131 15 0.6 1 15 132 10 0.6 1 8 2 133 16 0.6 1 14 2 134 25 0.6 1 18 7 135 25 0.6 1 13 12 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R1.fq.gz ============================================= 40743756 sequences processed in total