SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_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_17_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1882.20 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 58,612,409 Reads with adapters: 24,942,134 (42.6%) Reads written (passing filters): 58,612,409 (100.0%) Total basepairs processed: 7,367,240,322 bp Quality-trimmed: 2,008,699 bp (0.0%) Total written (filtered): 7,335,778,634 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24942134 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.4% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22192488 14653102.2 0 22192488 2 1784824 3663275.6 0 1784824 3 509781 915818.9 0 509781 4 336912 228954.7 0 336912 5 64715 57238.7 0 64715 6 15565 14309.7 0 15565 7 11496 3577.4 0 11496 8 8910 894.4 0 8910 9 2289 223.6 0 1884 405 10 14019 55.9 1 12878 1141 11 169 14.0 1 18 151 12 47 3.5 1 13 34 13 5 0.9 1 1 4 14 8 0.9 1 5 3 15 4 0.9 1 1 3 16 3 0.9 1 1 2 17 13 0.9 1 9 4 18 6 0.9 1 4 2 19 8 0.9 1 4 4 20 4 0.9 1 0 4 21 7 0.9 1 5 2 22 6 0.9 1 3 3 23 4 0.9 1 3 1 24 14 0.9 1 6 8 25 5 0.9 1 3 2 26 4 0.9 1 2 2 27 3 0.9 1 1 2 28 4 0.9 1 2 2 29 2 0.9 1 1 1 30 6 0.9 1 4 2 31 1 0.9 1 1 32 10 0.9 1 5 5 33 13 0.9 1 6 7 34 2 0.9 1 1 1 35 7 0.9 1 3 4 36 2 0.9 1 2 38 7 0.9 1 6 1 39 4 0.9 1 1 3 40 2 0.9 1 0 2 42 4 0.9 1 1 3 43 3 0.9 1 2 1 44 3 0.9 1 1 2 45 6 0.9 1 4 2 46 6 0.9 1 2 4 47 5 0.9 1 4 1 48 6 0.9 1 4 2 49 6 0.9 1 3 3 50 2 0.9 1 2 51 2 0.9 1 1 1 52 4 0.9 1 3 1 53 10 0.9 1 7 3 54 1 0.9 1 1 55 3 0.9 1 3 56 5 0.9 1 5 57 7 0.9 1 3 4 58 3 0.9 1 1 2 59 4 0.9 1 3 1 60 12 0.9 1 5 7 61 4 0.9 1 4 62 3 0.9 1 3 63 10 0.9 1 7 3 64 5 0.9 1 4 1 65 1 0.9 1 0 1 66 7 0.9 1 6 1 67 3 0.9 1 3 68 3 0.9 1 3 69 4 0.9 1 4 70 6 0.9 1 6 71 4 0.9 1 3 1 72 3 0.9 1 2 1 73 5 0.9 1 2 3 74 4 0.9 1 3 1 75 3 0.9 1 2 1 76 6 0.9 1 3 3 77 7 0.9 1 4 3 78 5 0.9 1 4 1 79 6 0.9 1 5 1 80 5 0.9 1 5 81 4 0.9 1 3 1 82 2 0.9 1 0 2 83 6 0.9 1 2 4 84 8 0.9 1 8 85 7 0.9 1 5 2 86 3 0.9 1 3 87 7 0.9 1 5 2 88 5 0.9 1 3 2 89 9 0.9 1 4 5 90 7 0.9 1 5 2 91 11 0.9 1 8 3 92 9 0.9 1 9 93 6 0.9 1 5 1 94 5 0.9 1 4 1 95 4 0.9 1 2 2 96 9 0.9 1 9 97 12 0.9 1 9 3 98 3 0.9 1 3 99 6 0.9 1 5 1 100 8 0.9 1 7 1 101 9 0.9 1 8 1 102 5 0.9 1 4 1 103 3 0.9 1 3 104 5 0.9 1 5 105 6 0.9 1 4 2 106 6 0.9 1 5 1 107 8 0.9 1 5 3 108 13 0.9 1 11 2 109 13 0.9 1 12 1 110 5 0.9 1 5 111 11 0.9 1 11 112 8 0.9 1 5 3 113 6 0.9 1 6 114 9 0.9 1 6 3 115 15 0.9 1 13 2 116 8 0.9 1 8 117 17 0.9 1 12 5 118 10 0.9 1 8 2 119 10 0.9 1 7 3 120 21 0.9 1 18 3 121 8 0.9 1 8 122 10 0.9 1 9 1 123 12 0.9 1 11 1 124 9 0.9 1 8 1 125 17 0.9 1 15 2 126 10 0.9 1 8 2 127 27 0.9 1 26 1 128 20 0.9 1 19 1 129 17 0.9 1 14 3 130 16 0.9 1 14 2 131 12 0.9 1 10 2 132 38 0.9 1 32 6 133 15 0.9 1 11 4 134 25 0.9 1 17 8 135 24 0.9 1 11 13 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R2.fq.gz ============================================= 58612409 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 58612409 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 304716 (0.52%)