SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_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_24_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1767.65 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 53,154,280 Reads with adapters: 22,971,054 (43.2%) Reads written (passing filters): 53,154,280 (100.0%) Total basepairs processed: 6,721,606,596 bp Quality-trimmed: 2,105,426 bp (0.0%) Total written (filtered): 6,692,511,074 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22971054 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20528839 13288570.0 0 20528839 2 1576070 3322142.5 0 1576070 3 464029 830535.6 0 464029 4 301169 207633.9 0 301169 5 54394 51908.5 0 54394 6 13620 12977.1 0 13620 7 10129 3244.3 0 10129 8 7521 811.1 0 7521 9 2045 202.8 0 1651 394 10 12162 50.7 1 11158 1004 11 139 12.7 1 19 120 12 37 3.2 1 7 30 13 10 0.8 1 1 9 14 3 0.8 1 2 1 15 2 0.8 1 0 2 16 1 0.8 1 1 17 4 0.8 1 2 2 18 3 0.8 1 2 1 19 6 0.8 1 2 4 20 4 0.8 1 2 2 22 3 0.8 1 2 1 24 4 0.8 1 0 4 25 7 0.8 1 3 4 26 3 0.8 1 0 3 27 2 0.8 1 2 28 5 0.8 1 2 3 29 1 0.8 1 0 1 30 5 0.8 1 3 2 31 2 0.8 1 2 32 6 0.8 1 4 2 33 3 0.8 1 0 3 34 6 0.8 1 5 1 35 1 0.8 1 1 36 6 0.8 1 3 3 37 1 0.8 1 1 38 6 0.8 1 4 2 39 3 0.8 1 1 2 40 12 0.8 1 6 6 41 1 0.8 1 1 42 6 0.8 1 5 1 43 2 0.8 1 0 2 44 3 0.8 1 1 2 45 6 0.8 1 5 1 46 2 0.8 1 1 1 47 5 0.8 1 4 1 48 4 0.8 1 2 2 49 4 0.8 1 4 50 1 0.8 1 0 1 51 7 0.8 1 4 3 52 2 0.8 1 1 1 53 3 0.8 1 2 1 54 3 0.8 1 2 1 55 2 0.8 1 2 56 5 0.8 1 2 3 57 4 0.8 1 4 58 4 0.8 1 1 3 59 1 0.8 1 1 60 7 0.8 1 4 3 61 2 0.8 1 1 1 62 3 0.8 1 3 63 3 0.8 1 2 1 64 3 0.8 1 2 1 65 5 0.8 1 3 2 66 6 0.8 1 3 3 67 6 0.8 1 3 3 68 2 0.8 1 0 2 69 5 0.8 1 4 1 70 2 0.8 1 2 71 2 0.8 1 0 2 72 4 0.8 1 4 73 3 0.8 1 1 2 74 9 0.8 1 6 3 76 7 0.8 1 6 1 77 5 0.8 1 3 2 78 9 0.8 1 9 79 5 0.8 1 5 80 7 0.8 1 7 81 7 0.8 1 4 3 82 4 0.8 1 2 2 83 3 0.8 1 2 1 84 8 0.8 1 5 3 85 8 0.8 1 7 1 86 8 0.8 1 7 1 87 6 0.8 1 4 2 88 6 0.8 1 3 3 90 7 0.8 1 5 2 91 3 0.8 1 3 92 8 0.8 1 8 93 9 0.8 1 6 3 94 8 0.8 1 5 3 95 3 0.8 1 2 1 96 7 0.8 1 4 3 97 6 0.8 1 5 1 98 10 0.8 1 8 2 99 11 0.8 1 11 100 10 0.8 1 6 4 101 18 0.8 1 16 2 102 9 0.8 1 7 2 103 9 0.8 1 9 104 3 0.8 1 2 1 105 9 0.8 1 9 106 10 0.8 1 9 1 107 6 0.8 1 4 2 108 14 0.8 1 12 2 109 8 0.8 1 7 1 110 13 0.8 1 10 3 111 10 0.8 1 8 2 112 7 0.8 1 5 2 113 11 0.8 1 9 2 114 12 0.8 1 10 2 115 9 0.8 1 7 2 116 13 0.8 1 11 2 117 12 0.8 1 11 1 118 16 0.8 1 14 2 119 8 0.8 1 8 120 12 0.8 1 10 2 121 16 0.8 1 13 3 122 16 0.8 1 15 1 123 11 0.8 1 8 3 124 14 0.8 1 13 1 125 17 0.8 1 15 2 126 13 0.8 1 13 127 22 0.8 1 21 1 128 16 0.8 1 13 3 129 20 0.8 1 19 1 130 20 0.8 1 16 4 131 29 0.8 1 27 2 132 25 0.8 1 20 5 133 18 0.8 1 13 5 134 24 0.8 1 14 10 135 29 0.8 1 13 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R2.fq.gz ============================================= 53154280 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 53154280 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 231736 (0.44%)