SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_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_20_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1737.72 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 54,311,933 Reads with adapters: 23,519,270 (43.3%) Reads written (passing filters): 54,311,933 (100.0%) Total basepairs processed: 6,895,076,635 bp Quality-trimmed: 1,433,956 bp (0.0%) Total written (filtered): 6,866,031,990 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23519270 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 9.9% G: 6.2% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20991923 13577983.2 0 20991923 2 1654391 3394495.8 0 1654391 3 474601 848624.0 0 474601 4 306931 212156.0 0 306931 5 48854 53039.0 0 48854 6 12498 13259.7 0 12498 7 8779 3314.9 0 8779 8 6824 828.7 0 6824 9 1898 207.2 0 1449 449 10 11483 51.8 1 10532 951 11 146 12.9 1 20 126 12 49 3.2 1 14 35 13 11 0.8 1 3 8 14 3 0.8 1 1 2 15 5 0.8 1 4 1 16 2 0.8 1 0 2 17 6 0.8 1 4 2 18 4 0.8 1 4 19 3 0.8 1 1 2 20 1 0.8 1 0 1 21 1 0.8 1 1 22 5 0.8 1 2 3 23 2 0.8 1 1 1 24 4 0.8 1 2 2 25 1 0.8 1 1 26 2 0.8 1 1 1 27 5 0.8 1 3 2 28 1 0.8 1 1 29 3 0.8 1 2 1 31 1 0.8 1 1 32 5 0.8 1 4 1 33 4 0.8 1 1 3 34 2 0.8 1 1 1 35 4 0.8 1 3 1 36 3 0.8 1 2 1 37 4 0.8 1 4 38 1 0.8 1 1 39 6 0.8 1 6 40 3 0.8 1 2 1 41 6 0.8 1 5 1 42 1 0.8 1 0 1 44 2 0.8 1 1 1 45 3 0.8 1 3 46 1 0.8 1 1 47 6 0.8 1 5 1 48 2 0.8 1 2 49 2 0.8 1 0 2 50 2 0.8 1 1 1 51 1 0.8 1 1 52 1 0.8 1 1 53 7 0.8 1 4 3 54 1 0.8 1 0 1 55 5 0.8 1 2 3 56 4 0.8 1 1 3 57 2 0.8 1 2 58 2 0.8 1 2 59 2 0.8 1 2 60 3 0.8 1 3 61 1 0.8 1 0 1 62 3 0.8 1 3 64 7 0.8 1 5 2 65 1 0.8 1 1 66 2 0.8 1 2 67 2 0.8 1 1 1 68 1 0.8 1 1 69 3 0.8 1 3 70 7 0.8 1 5 2 71 6 0.8 1 6 72 9 0.8 1 8 1 73 4 0.8 1 2 2 74 3 0.8 1 3 75 2 0.8 1 2 76 6 0.8 1 5 1 77 8 0.8 1 5 3 78 6 0.8 1 2 4 79 2 0.8 1 1 1 80 5 0.8 1 5 81 4 0.8 1 4 82 5 0.8 1 5 83 1 0.8 1 1 84 4 0.8 1 4 85 9 0.8 1 7 2 86 8 0.8 1 6 2 87 5 0.8 1 5 88 5 0.8 1 4 1 89 5 0.8 1 3 2 90 5 0.8 1 4 1 91 7 0.8 1 6 1 92 8 0.8 1 8 93 4 0.8 1 4 94 2 0.8 1 2 95 8 0.8 1 7 1 96 8 0.8 1 5 3 97 15 0.8 1 11 4 98 6 0.8 1 6 99 6 0.8 1 6 100 5 0.8 1 4 1 101 9 0.8 1 8 1 102 11 0.8 1 11 103 3 0.8 1 2 1 104 10 0.8 1 8 2 105 4 0.8 1 3 1 106 6 0.8 1 6 107 9 0.8 1 8 1 108 14 0.8 1 10 4 109 12 0.8 1 12 110 15 0.8 1 14 1 111 9 0.8 1 6 3 112 6 0.8 1 4 2 113 12 0.8 1 11 1 114 15 0.8 1 15 115 8 0.8 1 5 3 116 10 0.8 1 9 1 117 11 0.8 1 10 1 118 13 0.8 1 12 1 119 16 0.8 1 14 2 120 18 0.8 1 16 2 121 12 0.8 1 10 2 122 25 0.8 1 21 4 123 2 0.8 1 2 124 17 0.8 1 16 1 125 13 0.8 1 12 1 126 17 0.8 1 14 3 127 31 0.8 1 29 2 128 25 0.8 1 21 4 129 20 0.8 1 18 2 130 20 0.8 1 17 3 131 27 0.8 1 21 6 132 22 0.8 1 20 2 133 33 0.8 1 26 7 134 29 0.8 1 24 5 135 46 0.8 1 14 32 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R2.fq.gz ============================================= 54311933 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 54311933 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 227036 (0.42%)