SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_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_6_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1753.56 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 54,279,403 Reads with adapters: 23,389,569 (43.1%) Reads written (passing filters): 54,279,403 (100.0%) Total basepairs processed: 6,864,471,929 bp Quality-trimmed: 1,982,834 bp (0.0%) Total written (filtered): 6,834,977,157 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23389569 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.2% G: 6.1% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20894172 13569850.8 0 20894172 2 1616291 3392462.7 0 1616291 3 469462 848115.7 0 469462 4 305433 212028.9 0 305433 5 55463 53007.2 0 55463 6 13979 13251.8 0 13979 7 9891 3313.0 0 9891 8 7745 828.2 0 7745 9 2130 207.1 0 1675 455 10 13659 51.8 1 12616 1043 11 191 12.9 1 20 171 12 40 3.2 1 14 26 13 9 0.8 1 3 6 14 2 0.8 1 0 2 15 1 0.8 1 0 1 16 7 0.8 1 4 3 17 5 0.8 1 3 2 18 1 0.8 1 1 19 6 0.8 1 4 2 20 7 0.8 1 5 2 22 3 0.8 1 2 1 23 2 0.8 1 2 24 6 0.8 1 2 4 25 3 0.8 1 2 1 26 7 0.8 1 3 4 27 6 0.8 1 6 28 8 0.8 1 4 4 29 6 0.8 1 3 3 30 5 0.8 1 1 4 32 4 0.8 1 1 3 33 2 0.8 1 1 1 34 7 0.8 1 1 6 35 7 0.8 1 3 4 36 6 0.8 1 6 37 5 0.8 1 2 3 38 3 0.8 1 2 1 39 3 0.8 1 2 1 40 8 0.8 1 5 3 41 4 0.8 1 3 1 42 8 0.8 1 5 3 43 8 0.8 1 6 2 44 3 0.8 1 1 2 45 8 0.8 1 6 2 46 7 0.8 1 3 4 47 7 0.8 1 4 3 48 4 0.8 1 4 49 4 0.8 1 4 50 5 0.8 1 5 51 4 0.8 1 2 2 52 1 0.8 1 0 1 53 3 0.8 1 2 1 54 2 0.8 1 1 1 55 12 0.8 1 6 6 56 5 0.8 1 4 1 57 2 0.8 1 2 58 6 0.8 1 5 1 59 5 0.8 1 2 3 60 2 0.8 1 1 1 61 2 0.8 1 1 1 62 5 0.8 1 5 63 1 0.8 1 1 64 9 0.8 1 9 65 4 0.8 1 4 66 5 0.8 1 3 2 67 4 0.8 1 4 68 2 0.8 1 2 69 8 0.8 1 7 1 70 5 0.8 1 3 2 71 7 0.8 1 4 3 72 4 0.8 1 3 1 73 8 0.8 1 5 3 74 11 0.8 1 9 2 75 9 0.8 1 8 1 76 7 0.8 1 6 1 77 9 0.8 1 6 3 78 11 0.8 1 7 4 79 6 0.8 1 5 1 80 5 0.8 1 4 1 81 10 0.8 1 6 4 82 5 0.8 1 4 1 83 8 0.8 1 7 1 84 10 0.8 1 8 2 85 6 0.8 1 6 86 5 0.8 1 4 1 87 13 0.8 1 9 4 88 7 0.8 1 6 1 89 13 0.8 1 10 3 90 9 0.8 1 6 3 91 7 0.8 1 6 1 92 4 0.8 1 4 93 5 0.8 1 3 2 94 11 0.8 1 10 1 95 12 0.8 1 10 2 96 8 0.8 1 8 97 7 0.8 1 6 1 98 12 0.8 1 11 1 99 11 0.8 1 9 2 100 7 0.8 1 6 1 101 8 0.8 1 6 2 102 6 0.8 1 6 103 12 0.8 1 12 104 6 0.8 1 6 105 16 0.8 1 15 1 106 16 0.8 1 11 5 107 6 0.8 1 5 1 108 18 0.8 1 13 5 109 13 0.8 1 13 110 14 0.8 1 13 1 111 14 0.8 1 12 2 112 11 0.8 1 11 113 20 0.8 1 20 114 12 0.8 1 10 2 115 13 0.8 1 9 4 116 17 0.8 1 15 2 117 17 0.8 1 17 118 19 0.8 1 19 119 20 0.8 1 15 5 120 19 0.8 1 17 2 121 23 0.8 1 20 3 122 12 0.8 1 9 3 123 13 0.8 1 9 4 124 9 0.8 1 8 1 125 16 0.8 1 13 3 126 19 0.8 1 14 5 127 12 0.8 1 10 2 128 16 0.8 1 14 2 129 28 0.8 1 26 2 130 19 0.8 1 16 3 131 28 0.8 1 28 132 31 0.8 1 27 4 133 25 0.8 1 22 3 134 29 0.8 1 17 12 135 35 0.8 1 7 28 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R2.fq.gz ============================================= 54279403 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 54279403 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 246739 (0.45%)