SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_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_17_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1852.70 s (32 µs/read; 1.90 M reads/minute). === Summary === Total reads processed: 58,612,409 Reads with adapters: 25,043,792 (42.7%) Reads written (passing filters): 58,612,409 (100.0%) Total basepairs processed: 7,368,913,020 bp Quality-trimmed: 1,953,416 bp (0.0%) Total written (filtered): 7,337,218,337 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25043792 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.5% T: 37.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22152651 14653102.2 0 22152651 2 1919505 3663275.6 0 1919505 3 518513 915818.9 0 518513 4 329859 228954.7 0 329859 5 66332 57238.7 0 66332 6 16516 14309.7 0 16516 7 12191 3577.4 0 12191 8 9163 894.4 0 9163 9 2338 223.6 0 1847 491 10 14730 55.9 1 13538 1192 11 197 14.0 1 33 164 12 109 3.5 1 50 59 13 7 0.9 1 3 4 14 36 0.9 1 22 14 15 4 0.9 1 1 3 16 30 0.9 1 20 10 17 2 0.9 1 1 1 18 52 0.9 1 32 20 19 66 0.9 1 43 23 20 5 0.9 1 2 3 21 6 0.9 1 3 3 22 5 0.9 1 2 3 23 36 0.9 1 25 11 24 51 0.9 1 35 16 25 2 0.9 1 2 26 26 0.9 1 19 7 27 21 0.9 1 16 5 28 4 0.9 1 2 2 29 22 0.9 1 11 11 30 32 0.9 1 27 5 31 31 0.9 1 24 7 32 7 0.9 1 5 2 33 29 0.9 1 22 7 34 9 0.9 1 7 2 35 12 0.9 1 7 5 36 18 0.9 1 14 4 37 19 0.9 1 11 8 38 9 0.9 1 6 3 39 15 0.9 1 13 2 40 20 0.9 1 13 7 41 15 0.9 1 13 2 42 24 0.9 1 20 4 43 28 0.9 1 20 8 44 31 0.9 1 27 4 45 12 0.9 1 9 3 46 14 0.9 1 9 5 47 4 0.9 1 2 2 48 34 0.9 1 30 4 49 11 0.9 1 10 1 50 6 0.9 1 4 2 51 13 0.9 1 10 3 52 41 0.9 1 31 10 53 4 0.9 1 3 1 54 9 0.9 1 7 2 55 29 0.9 1 19 10 56 18 0.9 1 11 7 57 5 0.9 1 4 1 58 8 0.9 1 6 2 59 21 0.9 1 18 3 60 2 0.9 1 1 1 61 2 0.9 1 2 62 19 0.9 1 15 4 63 7 0.9 1 7 64 2 0.9 1 2 65 9 0.9 1 9 66 20 0.9 1 16 4 67 3 0.9 1 1 2 68 7 0.9 1 7 69 6 0.9 1 5 1 70 4 0.9 1 1 3 71 5 0.9 1 5 72 9 0.9 1 6 3 73 9 0.9 1 8 1 74 9 0.9 1 8 1 75 6 0.9 1 3 3 76 8 0.9 1 5 3 77 8 0.9 1 7 1 78 8 0.9 1 7 1 79 6 0.9 1 4 2 80 10 0.9 1 8 2 81 7 0.9 1 5 2 82 8 0.9 1 6 2 83 11 0.9 1 10 1 84 8 0.9 1 6 2 85 7 0.9 1 5 2 86 10 0.9 1 5 5 87 5 0.9 1 5 88 7 0.9 1 5 2 89 5 0.9 1 5 90 5 0.9 1 4 1 91 11 0.9 1 9 2 92 9 0.9 1 6 3 93 9 0.9 1 8 1 94 8 0.9 1 7 1 95 7 0.9 1 6 1 96 12 0.9 1 8 4 97 9 0.9 1 6 3 98 9 0.9 1 7 2 99 8 0.9 1 6 2 100 6 0.9 1 2 4 101 5 0.9 1 4 1 102 6 0.9 1 4 2 103 1 0.9 1 1 104 14 0.9 1 11 3 105 7 0.9 1 6 1 106 10 0.9 1 7 3 107 7 0.9 1 6 1 108 10 0.9 1 9 1 109 5 0.9 1 4 1 110 8 0.9 1 5 3 111 11 0.9 1 7 4 112 3 0.9 1 2 1 113 5 0.9 1 4 1 114 16 0.9 1 16 115 12 0.9 1 9 3 116 7 0.9 1 6 1 117 9 0.9 1 9 118 20 0.9 1 14 6 119 19 0.9 1 12 7 120 14 0.9 1 14 121 22 0.9 1 19 3 122 19 0.9 1 13 6 123 11 0.9 1 10 1 124 9 0.9 1 8 1 125 6 0.9 1 5 1 126 13 0.9 1 13 127 9 0.9 1 8 1 128 20 0.9 1 18 2 129 19 0.9 1 18 1 130 28 0.9 1 26 2 131 16 0.9 1 15 1 132 21 0.9 1 21 133 24 0.9 1 18 6 134 24 0.9 1 17 7 135 35 0.9 1 12 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R1.fq.gz ============================================= 58612409 sequences processed in total