SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_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_2_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1877.90 s (34 µs/read; 1.79 M reads/minute). === Summary === Total reads processed: 55,879,313 Reads with adapters: 24,638,835 (44.1%) Reads written (passing filters): 55,879,313 (100.0%) Total basepairs processed: 7,125,459,964 bp Quality-trimmed: 2,371,237 bp (0.0%) Total written (filtered): 7,094,372,704 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24638835 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.0% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22154035 13969828.2 0 22154035 2 1596677 3492457.1 0 1596677 3 490802 873114.3 0 490802 4 304016 218278.6 0 304016 5 49336 54569.6 0 49336 6 12245 13642.4 0 12245 7 8821 3410.6 0 8821 8 6824 852.7 0 6824 9 2088 213.2 0 1647 441 10 12805 53.3 1 11775 1030 11 138 13.3 1 22 116 12 34 3.3 1 6 28 13 6 0.8 1 3 3 14 9 0.8 1 6 3 15 5 0.8 1 3 2 16 1 0.8 1 0 1 17 7 0.8 1 2 5 18 5 0.8 1 4 1 19 6 0.8 1 1 5 20 2 0.8 1 1 1 21 10 0.8 1 6 4 22 3 0.8 1 0 3 23 3 0.8 1 3 24 4 0.8 1 1 3 25 7 0.8 1 5 2 26 1 0.8 1 0 1 27 4 0.8 1 3 1 28 7 0.8 1 4 3 29 3 0.8 1 2 1 30 5 0.8 1 2 3 31 5 0.8 1 4 1 32 8 0.8 1 5 3 33 5 0.8 1 4 1 34 6 0.8 1 3 3 35 5 0.8 1 2 3 36 9 0.8 1 7 2 37 3 0.8 1 1 2 38 3 0.8 1 1 2 39 3 0.8 1 3 40 1 0.8 1 1 42 3 0.8 1 1 2 43 3 0.8 1 1 2 44 6 0.8 1 4 2 45 2 0.8 1 1 1 46 3 0.8 1 1 2 47 9 0.8 1 6 3 48 4 0.8 1 4 49 5 0.8 1 5 50 1 0.8 1 1 51 1 0.8 1 1 52 3 0.8 1 3 53 2 0.8 1 2 54 4 0.8 1 4 55 1 0.8 1 0 1 56 8 0.8 1 2 6 57 2 0.8 1 1 1 58 7 0.8 1 7 59 5 0.8 1 5 60 9 0.8 1 7 2 61 5 0.8 1 3 2 62 6 0.8 1 5 1 63 6 0.8 1 4 2 64 2 0.8 1 2 65 5 0.8 1 5 66 10 0.8 1 3 7 67 1 0.8 1 1 68 5 0.8 1 4 1 69 5 0.8 1 3 2 70 2 0.8 1 2 71 8 0.8 1 6 2 72 9 0.8 1 7 2 73 8 0.8 1 6 2 74 7 0.8 1 5 2 75 5 0.8 1 5 76 4 0.8 1 4 77 4 0.8 1 4 78 6 0.8 1 3 3 79 9 0.8 1 9 80 4 0.8 1 3 1 81 8 0.8 1 5 3 82 9 0.8 1 9 83 9 0.8 1 8 1 84 12 0.8 1 9 3 85 6 0.8 1 4 2 86 4 0.8 1 4 87 5 0.8 1 5 88 7 0.8 1 7 89 7 0.8 1 5 2 90 5 0.8 1 5 91 7 0.8 1 5 2 92 8 0.8 1 6 2 93 8 0.8 1 5 3 94 9 0.8 1 7 2 95 8 0.8 1 5 3 96 6 0.8 1 3 3 97 9 0.8 1 9 98 10 0.8 1 8 2 99 6 0.8 1 6 100 5 0.8 1 5 101 5 0.8 1 4 1 102 3 0.8 1 3 103 4 0.8 1 3 1 104 3 0.8 1 3 105 10 0.8 1 10 106 9 0.8 1 8 1 107 10 0.8 1 9 1 108 15 0.8 1 15 109 15 0.8 1 12 3 110 11 0.8 1 8 3 111 11 0.8 1 8 3 112 13 0.8 1 12 1 113 8 0.8 1 6 2 114 8 0.8 1 7 1 115 14 0.8 1 11 3 116 14 0.8 1 12 2 117 11 0.8 1 10 1 118 20 0.8 1 15 5 119 15 0.8 1 13 2 120 18 0.8 1 16 2 121 14 0.8 1 13 1 122 14 0.8 1 13 1 123 21 0.8 1 18 3 124 22 0.8 1 17 5 125 23 0.8 1 20 3 126 19 0.8 1 15 4 127 16 0.8 1 15 1 128 15 0.8 1 14 1 129 18 0.8 1 17 1 130 28 0.8 1 25 3 131 31 0.8 1 27 4 132 19 0.8 1 14 5 133 20 0.8 1 15 5 134 26 0.8 1 16 10 135 38 0.8 1 17 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R2.fq.gz ============================================= 55879313 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 55879313 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 214944 (0.38%)