SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_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_19_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1896.57 s (38 µs/read; 1.57 M reads/minute). === Summary === Total reads processed: 49,611,452 Reads with adapters: 21,362,959 (43.1%) Reads written (passing filters): 49,611,452 (100.0%) Total basepairs processed: 6,252,863,959 bp Quality-trimmed: 1,776,907 bp (0.0%) Total written (filtered): 6,225,809,904 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21362959 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.4% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18933491 12402863.0 0 18933491 2 1613051 3100715.8 0 1613051 3 445071 775178.9 0 445071 4 275236 193794.7 0 275236 5 51936 48448.7 0 51936 6 13128 12112.2 0 13128 7 9175 3028.0 0 9175 8 6901 757.0 0 6901 9 1821 189.3 0 1428 393 10 11758 47.3 1 10773 985 11 162 11.8 1 27 135 12 60 3.0 1 22 38 13 7 0.7 1 2 5 14 23 0.7 1 13 10 15 5 0.7 1 3 2 16 20 0.7 1 17 3 18 40 0.7 1 24 16 19 30 0.7 1 19 11 20 2 0.7 1 1 1 21 1 0.7 1 1 22 1 0.7 1 1 23 24 0.7 1 14 10 24 20 0.7 1 15 5 25 3 0.7 1 2 1 26 8 0.7 1 5 3 27 5 0.7 1 5 28 1 0.7 1 0 1 29 8 0.7 1 4 4 30 15 0.7 1 10 5 31 21 0.7 1 15 6 32 4 0.7 1 3 1 33 15 0.7 1 10 5 34 7 0.7 1 1 6 35 10 0.7 1 6 4 36 10 0.7 1 7 3 37 9 0.7 1 5 4 38 19 0.7 1 9 10 39 16 0.7 1 10 6 40 5 0.7 1 4 1 41 14 0.7 1 9 5 42 9 0.7 1 7 2 43 10 0.7 1 5 5 44 18 0.7 1 13 5 45 3 0.7 1 3 46 11 0.7 1 8 3 47 5 0.7 1 5 48 21 0.7 1 16 5 49 13 0.7 1 6 7 50 13 0.7 1 6 7 51 11 0.7 1 6 5 52 16 0.7 1 14 2 53 5 0.7 1 5 54 5 0.7 1 5 55 20 0.7 1 13 7 56 10 0.7 1 8 2 57 1 0.7 1 1 58 5 0.7 1 4 1 59 9 0.7 1 6 3 60 1 0.7 1 1 61 2 0.7 1 2 62 11 0.7 1 7 4 63 2 0.7 1 2 64 7 0.7 1 5 2 65 3 0.7 1 0 3 66 10 0.7 1 8 2 67 5 0.7 1 4 1 68 8 0.7 1 6 2 69 7 0.7 1 6 1 70 3 0.7 1 3 71 4 0.7 1 1 3 72 4 0.7 1 3 1 73 6 0.7 1 2 4 74 2 0.7 1 2 75 3 0.7 1 2 1 76 7 0.7 1 5 2 77 13 0.7 1 9 4 78 7 0.7 1 6 1 79 6 0.7 1 3 3 80 8 0.7 1 6 2 81 7 0.7 1 7 82 2 0.7 1 1 1 83 6 0.7 1 4 2 84 1 0.7 1 0 1 85 11 0.7 1 11 86 10 0.7 1 5 5 87 4 0.7 1 4 88 9 0.7 1 6 3 89 7 0.7 1 7 90 6 0.7 1 4 2 91 7 0.7 1 5 2 92 2 0.7 1 2 93 5 0.7 1 5 94 1 0.7 1 1 95 4 0.7 1 4 96 7 0.7 1 7 97 3 0.7 1 2 1 98 8 0.7 1 8 99 10 0.7 1 9 1 100 5 0.7 1 4 1 101 4 0.7 1 3 1 102 7 0.7 1 7 103 5 0.7 1 3 2 104 7 0.7 1 6 1 105 8 0.7 1 5 3 106 8 0.7 1 5 3 107 7 0.7 1 5 2 108 4 0.7 1 3 1 109 4 0.7 1 3 1 110 5 0.7 1 3 2 111 10 0.7 1 10 112 5 0.7 1 4 1 113 5 0.7 1 5 114 6 0.7 1 6 115 7 0.7 1 6 1 116 7 0.7 1 5 2 117 13 0.7 1 12 1 118 19 0.7 1 16 3 119 12 0.7 1 11 1 120 8 0.7 1 8 121 13 0.7 1 12 1 122 13 0.7 1 10 3 123 13 0.7 1 13 124 12 0.7 1 12 125 20 0.7 1 13 7 126 11 0.7 1 5 6 127 10 0.7 1 8 2 128 18 0.7 1 18 129 14 0.7 1 10 4 130 15 0.7 1 13 2 131 23 0.7 1 19 4 132 22 0.7 1 17 5 133 17 0.7 1 13 4 134 24 0.7 1 14 10 135 31 0.7 1 11 20 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R1.fq.gz ============================================= 49611452 sequences processed in total