SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.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_4_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1604.01 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 50,228,886 Reads with adapters: 21,636,567 (43.1%) Reads written (passing filters): 50,228,886 (100.0%) Total basepairs processed: 6,352,591,952 bp Quality-trimmed: 1,729,527 bp (0.0%) Total written (filtered): 6,325,433,799 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21636567 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.1% G: 6.0% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19340172 12557221.5 0 19340172 2 1494763 3139305.4 0 1494763 3 424673 784826.3 0 424673 4 279671 196206.6 0 279671 5 52568 49051.6 0 52568 6 13090 12262.9 0 13090 7 9143 3065.7 0 9143 8 6874 766.4 0 6874 9 1861 191.6 0 1473 388 10 12512 47.9 1 11560 952 11 148 12.0 1 21 127 12 37 3.0 1 14 23 13 13 0.7 1 5 8 14 7 0.7 1 3 4 15 1 0.7 1 1 16 2 0.7 1 0 2 17 2 0.7 1 0 2 18 2 0.7 1 2 19 10 0.7 1 4 6 20 4 0.7 1 2 2 21 2 0.7 1 2 22 4 0.7 1 3 1 23 7 0.7 1 5 2 24 5 0.7 1 4 1 25 4 0.7 1 2 2 26 1 0.7 1 1 27 1 0.7 1 1 28 3 0.7 1 1 2 29 3 0.7 1 1 2 30 7 0.7 1 5 2 31 3 0.7 1 2 1 32 2 0.7 1 0 2 33 2 0.7 1 2 34 9 0.7 1 5 4 36 3 0.7 1 2 1 37 3 0.7 1 2 1 38 3 0.7 1 2 1 40 11 0.7 1 10 1 41 4 0.7 1 3 1 42 5 0.7 1 4 1 43 2 0.7 1 0 2 44 6 0.7 1 3 3 45 7 0.7 1 6 1 46 1 0.7 1 1 47 5 0.7 1 2 3 48 2 0.7 1 1 1 49 4 0.7 1 2 2 50 3 0.7 1 2 1 51 5 0.7 1 5 52 4 0.7 1 3 1 53 5 0.7 1 2 3 54 6 0.7 1 5 1 55 5 0.7 1 4 1 56 3 0.7 1 2 1 57 4 0.7 1 3 1 58 5 0.7 1 4 1 59 2 0.7 1 1 1 60 5 0.7 1 3 2 61 5 0.7 1 4 1 62 5 0.7 1 4 1 63 6 0.7 1 3 3 64 3 0.7 1 3 65 6 0.7 1 3 3 66 4 0.7 1 3 1 67 1 0.7 1 1 68 5 0.7 1 5 69 4 0.7 1 4 70 7 0.7 1 6 1 71 8 0.7 1 8 72 5 0.7 1 3 2 73 6 0.7 1 3 3 74 9 0.7 1 7 2 75 1 0.7 1 1 76 2 0.7 1 2 77 3 0.7 1 2 1 78 3 0.7 1 3 79 9 0.7 1 5 4 80 11 0.7 1 10 1 81 3 0.7 1 3 82 5 0.7 1 5 83 3 0.7 1 3 84 14 0.7 1 11 3 85 4 0.7 1 4 86 10 0.7 1 8 2 87 5 0.7 1 4 1 88 7 0.7 1 5 2 89 8 0.7 1 8 90 11 0.7 1 7 4 91 6 0.7 1 6 92 7 0.7 1 5 2 93 7 0.7 1 7 94 5 0.7 1 5 95 10 0.7 1 8 2 96 12 0.7 1 9 3 97 9 0.7 1 7 2 98 9 0.7 1 5 4 99 11 0.7 1 10 1 100 10 0.7 1 9 1 101 7 0.7 1 6 1 102 9 0.7 1 7 2 103 13 0.7 1 11 2 104 3 0.7 1 3 105 7 0.7 1 7 106 5 0.7 1 5 107 10 0.7 1 8 2 108 11 0.7 1 8 3 109 16 0.7 1 15 1 110 12 0.7 1 12 111 8 0.7 1 6 2 112 21 0.7 1 19 2 113 11 0.7 1 9 2 114 16 0.7 1 15 1 115 8 0.7 1 8 116 18 0.7 1 17 1 117 10 0.7 1 6 4 118 20 0.7 1 15 5 119 18 0.7 1 15 3 120 11 0.7 1 10 1 121 20 0.7 1 20 122 19 0.7 1 14 5 123 15 0.7 1 14 1 124 32 0.7 1 22 10 125 16 0.7 1 16 126 23 0.7 1 21 2 127 21 0.7 1 15 6 128 15 0.7 1 10 5 129 23 0.7 1 18 5 130 24 0.7 1 19 5 131 26 0.7 1 23 3 132 29 0.7 1 24 5 133 31 0.7 1 24 7 134 33 0.7 1 22 11 135 38 0.7 1 13 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.fq.gz ============================================= 50228886 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 50228886 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 216426 (0.43%)