SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_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_13_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2073.70 s (38 µs/read; 1.57 M reads/minute). === Summary === Total reads processed: 54,135,312 Reads with adapters: 23,721,761 (43.8%) Reads written (passing filters): 54,135,312 (100.0%) Total basepairs processed: 6,877,739,495 bp Quality-trimmed: 2,137,120 bp (0.0%) Total written (filtered): 6,847,681,076 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23721761 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.4% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21118975 13533828.0 0 21118975 2 1726136 3383457.0 0 1726136 3 485217 845864.2 0 485217 4 294326 211466.1 0 294326 5 50975 52866.5 0 50975 6 13477 13216.6 0 13477 7 9619 3304.2 0 9619 8 7050 826.0 0 7050 9 1973 206.5 0 1544 429 10 12595 51.6 1 11537 1058 11 162 12.9 1 26 136 12 46 3.2 1 15 31 13 5 0.8 1 3 2 14 10 0.8 1 6 4 15 4 0.8 1 1 3 16 11 0.8 1 6 5 17 2 0.8 1 2 18 15 0.8 1 9 6 19 14 0.8 1 7 7 20 3 0.8 1 2 1 21 9 0.8 1 7 2 22 3 0.8 1 1 2 23 13 0.8 1 10 3 24 9 0.8 1 4 5 25 3 0.8 1 2 1 26 5 0.8 1 2 3 27 3 0.8 1 3 28 5 0.8 1 3 2 29 6 0.8 1 5 1 30 9 0.8 1 4 5 31 12 0.8 1 7 5 32 4 0.8 1 2 2 33 4 0.8 1 2 2 34 2 0.8 1 2 35 6 0.8 1 3 3 36 9 0.8 1 6 3 37 3 0.8 1 3 38 7 0.8 1 2 5 39 9 0.8 1 9 40 7 0.8 1 5 2 41 5 0.8 1 3 2 42 3 0.8 1 3 43 6 0.8 1 4 2 44 6 0.8 1 3 3 45 6 0.8 1 2 4 46 5 0.8 1 2 3 47 4 0.8 1 3 1 48 4 0.8 1 3 1 49 4 0.8 1 4 50 6 0.8 1 5 1 51 3 0.8 1 3 52 10 0.8 1 9 1 53 3 0.8 1 2 1 54 7 0.8 1 5 2 55 5 0.8 1 3 2 56 8 0.8 1 6 2 57 6 0.8 1 5 1 58 3 0.8 1 3 59 6 0.8 1 4 2 60 3 0.8 1 2 1 61 8 0.8 1 5 3 62 5 0.8 1 4 1 63 2 0.8 1 1 1 64 5 0.8 1 3 2 65 4 0.8 1 3 1 66 6 0.8 1 4 2 67 6 0.8 1 4 2 68 3 0.8 1 2 1 69 6 0.8 1 5 1 70 8 0.8 1 7 1 71 4 0.8 1 2 2 72 5 0.8 1 5 73 5 0.8 1 4 1 74 5 0.8 1 4 1 75 6 0.8 1 6 76 1 0.8 1 1 77 5 0.8 1 3 2 78 5 0.8 1 4 1 79 1 0.8 1 0 1 80 5 0.8 1 4 1 81 10 0.8 1 7 3 82 2 0.8 1 2 83 6 0.8 1 5 1 84 8 0.8 1 7 1 85 7 0.8 1 7 86 9 0.8 1 7 2 87 10 0.8 1 8 2 88 14 0.8 1 9 5 89 9 0.8 1 7 2 90 15 0.8 1 11 4 91 11 0.8 1 5 6 92 9 0.8 1 8 1 93 5 0.8 1 5 94 13 0.8 1 12 1 95 13 0.8 1 11 2 96 4 0.8 1 4 97 6 0.8 1 2 4 98 6 0.8 1 3 3 99 13 0.8 1 11 2 100 8 0.8 1 8 101 12 0.8 1 11 1 102 8 0.8 1 7 1 103 11 0.8 1 6 5 104 6 0.8 1 5 1 105 12 0.8 1 12 106 15 0.8 1 15 107 7 0.8 1 6 1 108 13 0.8 1 13 109 8 0.8 1 8 110 14 0.8 1 13 1 111 12 0.8 1 11 1 112 17 0.8 1 15 2 113 15 0.8 1 13 2 114 8 0.8 1 8 115 10 0.8 1 9 1 116 9 0.8 1 8 1 117 10 0.8 1 9 1 118 28 0.8 1 24 4 119 13 0.8 1 12 1 120 22 0.8 1 16 6 121 10 0.8 1 6 4 122 25 0.8 1 21 4 123 25 0.8 1 18 7 124 16 0.8 1 14 2 125 19 0.8 1 18 1 126 13 0.8 1 12 1 127 14 0.8 1 13 1 128 28 0.8 1 27 1 129 29 0.8 1 25 4 130 38 0.8 1 33 5 131 22 0.8 1 17 5 132 32 0.8 1 30 2 133 28 0.8 1 22 6 134 34 0.8 1 23 11 135 59 0.8 1 22 37 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R1.fq.gz ============================================= 54135312 sequences processed in total