SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_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_11_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1850.90 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 57,092,207 Reads with adapters: 24,597,705 (43.1%) Reads written (passing filters): 57,092,207 (100.0%) Total basepairs processed: 7,192,359,667 bp Quality-trimmed: 2,438,054 bp (0.0%) Total written (filtered): 7,160,901,486 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24597705 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 6.2% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21938947 14273051.8 0 21938947 2 1725533 3568262.9 0 1725533 3 494996 892065.7 0 494996 4 325612 223016.4 0 325612 5 60444 55754.1 0 60444 6 15122 13938.5 0 15122 7 10970 3484.6 0 10970 8 8166 871.2 0 8166 9 2181 217.8 0 1742 439 10 13918 54.4 1 12775 1143 11 184 13.6 1 37 147 12 57 3.4 1 17 40 13 14 0.9 1 6 8 14 5 0.9 1 2 3 15 9 0.9 1 7 2 16 3 0.9 1 2 1 17 3 0.9 1 0 3 18 6 0.9 1 4 2 19 9 0.9 1 6 3 20 9 0.9 1 7 2 21 10 0.9 1 4 6 22 8 0.9 1 4 4 23 4 0.9 1 3 1 24 8 0.9 1 6 2 25 12 0.9 1 8 4 26 4 0.9 1 3 1 27 7 0.9 1 6 1 28 5 0.9 1 4 1 29 6 0.9 1 4 2 30 7 0.9 1 3 4 31 8 0.9 1 6 2 32 6 0.9 1 4 2 33 5 0.9 1 3 2 34 6 0.9 1 5 1 35 7 0.9 1 2 5 36 5 0.9 1 3 2 37 8 0.9 1 7 1 38 9 0.9 1 5 4 39 7 0.9 1 3 4 40 8 0.9 1 7 1 41 3 0.9 1 2 1 42 4 0.9 1 3 1 43 7 0.9 1 6 1 44 8 0.9 1 6 2 45 9 0.9 1 7 2 46 8 0.9 1 6 2 47 4 0.9 1 3 1 48 2 0.9 1 1 1 49 16 0.9 1 14 2 50 8 0.9 1 7 1 51 6 0.9 1 4 2 52 9 0.9 1 4 5 53 9 0.9 1 8 1 54 6 0.9 1 3 3 55 5 0.9 1 3 2 56 17 0.9 1 12 5 57 12 0.9 1 8 4 58 9 0.9 1 8 1 59 5 0.9 1 5 60 8 0.9 1 8 61 7 0.9 1 6 1 62 7 0.9 1 5 2 63 9 0.9 1 6 3 64 7 0.9 1 6 1 65 8 0.9 1 5 3 66 13 0.9 1 9 4 67 9 0.9 1 5 4 68 6 0.9 1 5 1 69 15 0.9 1 13 2 70 10 0.9 1 8 2 71 8 0.9 1 5 3 72 6 0.9 1 4 2 73 9 0.9 1 5 4 74 8 0.9 1 7 1 75 9 0.9 1 9 76 13 0.9 1 10 3 77 6 0.9 1 5 1 78 10 0.9 1 4 6 79 12 0.9 1 11 1 80 18 0.9 1 16 2 81 7 0.9 1 7 82 1 0.9 1 1 83 12 0.9 1 8 4 84 3 0.9 1 3 85 14 0.9 1 12 2 86 10 0.9 1 9 1 87 7 0.9 1 6 1 88 9 0.9 1 9 89 12 0.9 1 11 1 90 10 0.9 1 9 1 91 18 0.9 1 16 2 92 17 0.9 1 11 6 93 8 0.9 1 7 1 94 18 0.9 1 14 4 95 10 0.9 1 7 3 96 17 0.9 1 12 5 97 13 0.9 1 11 2 98 17 0.9 1 17 99 11 0.9 1 11 100 5 0.9 1 5 101 13 0.9 1 11 2 102 19 0.9 1 16 3 103 9 0.9 1 8 1 104 15 0.9 1 14 1 105 13 0.9 1 9 4 106 12 0.9 1 12 107 15 0.9 1 13 2 108 12 0.9 1 11 1 109 9 0.9 1 7 2 110 18 0.9 1 16 2 111 21 0.9 1 19 2 112 9 0.9 1 7 2 113 27 0.9 1 18 9 114 21 0.9 1 16 5 115 22 0.9 1 18 4 116 15 0.9 1 13 2 117 17 0.9 1 15 2 118 20 0.9 1 19 1 119 17 0.9 1 14 3 120 17 0.9 1 14 3 121 25 0.9 1 19 6 122 22 0.9 1 17 5 123 21 0.9 1 19 2 124 20 0.9 1 14 6 125 24 0.9 1 22 2 126 20 0.9 1 16 4 127 31 0.9 1 28 3 128 29 0.9 1 25 4 129 33 0.9 1 27 6 130 41 0.9 1 34 7 131 41 0.9 1 37 4 132 32 0.9 1 30 2 133 52 0.9 1 40 12 134 45 0.9 1 34 11 135 56 0.9 1 31 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R2.fq.gz ============================================= 57092207 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 57092207 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 284658 (0.50%)