SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_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_15_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1932.23 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 59,408,352 Reads with adapters: 25,648,945 (43.2%) Reads written (passing filters): 59,408,352 (100.0%) Total basepairs processed: 7,515,911,423 bp Quality-trimmed: 2,005,465 bp (0.0%) Total written (filtered): 7,483,739,706 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25648945 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.1% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22912081 14852088.0 0 22912081 2 1772714 3713022.0 0 1772714 3 516812 928255.5 0 516812 4 333951 232063.9 0 333951 5 62195 58016.0 0 62195 6 15010 14504.0 0 15010 7 10651 3626.0 0 10651 8 7911 906.5 0 7911 9 2232 226.6 0 1710 522 10 13847 56.7 1 12684 1163 11 170 14.2 1 19 151 12 58 3.5 1 12 46 13 13 0.9 1 4 9 15 7 0.9 1 6 1 16 3 0.9 1 3 17 7 0.9 1 3 4 18 3 0.9 1 1 2 19 6 0.9 1 2 4 20 4 0.9 1 1 3 21 3 0.9 1 3 22 4 0.9 1 1 3 23 6 0.9 1 4 2 24 10 0.9 1 4 6 25 4 0.9 1 2 2 26 6 0.9 1 3 3 27 4 0.9 1 2 2 28 5 0.9 1 2 3 29 2 0.9 1 1 1 30 12 0.9 1 7 5 31 5 0.9 1 5 32 11 0.9 1 6 5 33 9 0.9 1 8 1 34 9 0.9 1 5 4 35 6 0.9 1 4 2 36 7 0.9 1 3 4 37 3 0.9 1 3 38 6 0.9 1 6 39 6 0.9 1 4 2 40 5 0.9 1 4 1 41 6 0.9 1 6 42 7 0.9 1 4 3 43 4 0.9 1 2 2 44 12 0.9 1 5 7 45 6 0.9 1 4 2 46 2 0.9 1 1 1 47 6 0.9 1 5 1 48 12 0.9 1 9 3 49 11 0.9 1 8 3 50 2 0.9 1 2 51 7 0.9 1 5 2 52 2 0.9 1 1 1 53 8 0.9 1 8 54 5 0.9 1 4 1 55 4 0.9 1 3 1 56 4 0.9 1 4 57 4 0.9 1 4 58 4 0.9 1 3 1 59 6 0.9 1 3 3 60 12 0.9 1 6 6 61 6 0.9 1 4 2 62 1 0.9 1 1 63 12 0.9 1 10 2 64 8 0.9 1 6 2 65 4 0.9 1 4 66 10 0.9 1 8 2 67 8 0.9 1 8 68 10 0.9 1 10 69 5 0.9 1 5 70 9 0.9 1 7 2 71 7 0.9 1 5 2 72 4 0.9 1 4 73 5 0.9 1 5 74 3 0.9 1 2 1 75 9 0.9 1 8 1 76 11 0.9 1 10 1 77 4 0.9 1 4 78 6 0.9 1 4 2 79 10 0.9 1 9 1 80 13 0.9 1 11 2 81 5 0.9 1 5 82 3 0.9 1 3 83 9 0.9 1 8 1 84 12 0.9 1 11 1 85 8 0.9 1 7 1 86 8 0.9 1 7 1 87 10 0.9 1 8 2 88 12 0.9 1 10 2 89 4 0.9 1 4 90 11 0.9 1 7 4 91 7 0.9 1 7 92 12 0.9 1 8 4 93 15 0.9 1 13 2 94 10 0.9 1 9 1 95 4 0.9 1 2 2 96 8 0.9 1 8 97 11 0.9 1 8 3 98 9 0.9 1 7 2 99 9 0.9 1 7 2 100 11 0.9 1 10 1 101 10 0.9 1 8 2 102 4 0.9 1 3 1 103 10 0.9 1 8 2 104 7 0.9 1 7 105 13 0.9 1 10 3 106 16 0.9 1 13 3 107 11 0.9 1 11 108 21 0.9 1 20 1 109 15 0.9 1 14 1 110 11 0.9 1 8 3 111 8 0.9 1 8 112 12 0.9 1 11 1 113 17 0.9 1 15 2 114 14 0.9 1 14 115 26 0.9 1 17 9 116 21 0.9 1 20 1 117 17 0.9 1 17 118 31 0.9 1 25 6 119 28 0.9 1 22 6 120 19 0.9 1 17 2 121 15 0.9 1 15 122 17 0.9 1 14 3 123 20 0.9 1 17 3 124 16 0.9 1 16 125 18 0.9 1 13 5 126 22 0.9 1 18 4 127 22 0.9 1 20 2 128 22 0.9 1 21 1 129 15 0.9 1 13 2 130 42 0.9 1 36 6 131 41 0.9 1 31 10 132 28 0.9 1 25 3 133 32 0.9 1 23 9 134 33 0.9 1 23 10 135 46 0.9 1 24 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R2.fq.gz ============================================= 59408352 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 59408352 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 270791 (0.46%)