SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_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_22_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1915.16 s (40 µs/read; 1.50 M reads/minute). === Summary === Total reads processed: 47,948,800 Reads with adapters: 20,603,226 (43.0%) Reads written (passing filters): 47,948,800 (100.0%) Total basepairs processed: 6,053,610,438 bp Quality-trimmed: 2,087,826 bp (0.0%) Total written (filtered): 6,027,275,695 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20603226 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.3% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18375358 11987200.0 0 18375358 2 1443882 2996800.0 0 1443882 3 420748 749200.0 0 420748 4 272111 187300.0 0 272111 5 49381 46825.0 0 49381 6 12266 11706.2 0 12266 7 9063 2926.6 0 9063 8 6684 731.6 0 6684 9 1756 182.9 0 1408 348 10 11040 45.7 1 10119 921 11 126 11.4 1 15 111 12 46 2.9 1 9 37 13 10 0.7 1 3 7 14 6 0.7 1 1 5 15 7 0.7 1 3 4 16 2 0.7 1 2 17 4 0.7 1 3 1 18 1 0.7 1 1 19 3 0.7 1 2 1 20 3 0.7 1 3 21 2 0.7 1 2 22 2 0.7 1 1 1 23 5 0.7 1 2 3 24 7 0.7 1 3 4 25 5 0.7 1 2 3 26 2 0.7 1 0 2 27 5 0.7 1 2 3 28 4 0.7 1 3 1 29 3 0.7 1 2 1 30 3 0.7 1 3 31 3 0.7 1 2 1 32 8 0.7 1 3 5 33 4 0.7 1 2 2 34 7 0.7 1 6 1 35 2 0.7 1 1 1 36 7 0.7 1 3 4 37 7 0.7 1 4 3 38 3 0.7 1 1 2 39 7 0.7 1 4 3 40 5 0.7 1 3 2 41 4 0.7 1 2 2 42 2 0.7 1 1 1 43 3 0.7 1 2 1 44 7 0.7 1 4 3 45 7 0.7 1 5 2 46 3 0.7 1 2 1 47 2 0.7 1 1 1 48 9 0.7 1 6 3 49 7 0.7 1 6 1 50 3 0.7 1 1 2 51 5 0.7 1 4 1 52 2 0.7 1 2 53 5 0.7 1 2 3 54 3 0.7 1 3 55 2 0.7 1 1 1 56 3 0.7 1 3 57 7 0.7 1 4 3 58 3 0.7 1 0 3 59 4 0.7 1 1 3 60 9 0.7 1 7 2 61 7 0.7 1 5 2 62 3 0.7 1 3 63 5 0.7 1 3 2 64 8 0.7 1 6 2 65 2 0.7 1 2 66 6 0.7 1 1 5 67 3 0.7 1 2 1 68 5 0.7 1 4 1 69 6 0.7 1 5 1 70 8 0.7 1 6 2 71 3 0.7 1 2 1 72 2 0.7 1 2 73 5 0.7 1 4 1 75 3 0.7 1 3 76 3 0.7 1 2 1 77 3 0.7 1 3 78 2 0.7 1 0 2 79 5 0.7 1 4 1 80 4 0.7 1 4 81 7 0.7 1 4 3 82 1 0.7 1 1 83 3 0.7 1 0 3 84 2 0.7 1 1 1 85 6 0.7 1 3 3 86 4 0.7 1 3 1 87 4 0.7 1 4 88 11 0.7 1 8 3 89 3 0.7 1 3 90 6 0.7 1 5 1 91 3 0.7 1 3 92 3 0.7 1 3 93 9 0.7 1 9 94 5 0.7 1 4 1 95 3 0.7 1 2 1 96 5 0.7 1 5 97 3 0.7 1 3 98 10 0.7 1 6 4 99 5 0.7 1 4 1 100 11 0.7 1 9 2 101 5 0.7 1 4 1 102 4 0.7 1 4 103 2 0.7 1 2 104 6 0.7 1 6 105 8 0.7 1 7 1 106 6 0.7 1 4 2 107 5 0.7 1 5 108 5 0.7 1 2 3 109 5 0.7 1 5 110 8 0.7 1 8 111 7 0.7 1 7 112 6 0.7 1 5 1 113 10 0.7 1 8 2 114 8 0.7 1 6 2 115 5 0.7 1 5 116 5 0.7 1 5 117 5 0.7 1 1 4 118 9 0.7 1 8 1 119 10 0.7 1 8 2 120 15 0.7 1 13 2 121 11 0.7 1 10 1 122 12 0.7 1 11 1 123 9 0.7 1 6 3 124 11 0.7 1 11 125 14 0.7 1 11 3 126 15 0.7 1 12 3 127 8 0.7 1 7 1 128 16 0.7 1 11 5 129 21 0.7 1 21 130 13 0.7 1 13 131 20 0.7 1 18 2 132 18 0.7 1 17 1 133 20 0.7 1 16 4 134 10 0.7 1 6 4 135 29 0.7 1 8 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R2.fq.gz ============================================= 47948800 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 47948800 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 223618 (0.47%)