SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.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_21_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1734.86 s (34 µs/read; 1.78 M reads/minute). === Summary === Total reads processed: 51,337,098 Reads with adapters: 22,468,074 (43.8%) Reads written (passing filters): 51,337,098 (100.0%) Total basepairs processed: 6,504,759,787 bp Quality-trimmed: 2,335,656 bp (0.0%) Total written (filtered): 6,475,942,942 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22468074 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.6% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19979505 12834274.5 0 19979505 2 1650411 3208568.6 0 1650411 3 470020 802142.2 0 470020 4 279846 200535.5 0 279846 5 46716 50133.9 0 46716 6 12187 12533.5 0 12187 7 8532 3133.4 0 8532 8 5998 783.3 0 5998 9 1655 195.8 0 1276 379 10 10922 49.0 1 9939 983 11 175 12.2 1 38 137 12 114 3.1 1 48 66 13 13 0.8 1 5 8 14 35 0.8 1 26 9 15 5 0.8 1 3 2 16 40 0.8 1 28 12 17 3 0.8 1 3 18 59 0.8 1 45 14 19 107 0.8 1 73 34 20 4 0.8 1 3 1 21 1 0.8 1 1 22 8 0.8 1 3 5 23 49 0.8 1 36 13 24 56 0.8 1 48 8 25 3 0.8 1 1 2 26 28 0.8 1 23 5 27 20 0.8 1 19 1 28 1 0.8 1 1 29 24 0.8 1 14 10 30 33 0.8 1 21 12 31 48 0.8 1 37 11 32 12 0.8 1 7 5 33 43 0.8 1 32 11 34 16 0.8 1 11 5 35 16 0.8 1 10 6 36 43 0.8 1 33 10 37 26 0.8 1 14 12 38 9 0.8 1 8 1 39 10 0.8 1 6 4 40 21 0.8 1 15 6 41 10 0.8 1 8 2 42 37 0.8 1 28 9 43 25 0.8 1 19 6 44 30 0.8 1 24 6 45 9 0.8 1 8 1 46 19 0.8 1 17 2 47 5 0.8 1 4 1 48 36 0.8 1 26 10 49 24 0.8 1 15 9 50 26 0.8 1 20 6 51 18 0.8 1 16 2 52 51 0.8 1 41 10 53 11 0.8 1 10 1 54 4 0.8 1 3 1 55 35 0.8 1 31 4 56 29 0.8 1 25 4 57 7 0.8 1 4 3 58 8 0.8 1 6 2 59 21 0.8 1 17 4 60 5 0.8 1 5 61 9 0.8 1 6 3 62 25 0.8 1 21 4 63 4 0.8 1 3 1 64 9 0.8 1 5 4 65 12 0.8 1 12 66 21 0.8 1 17 4 67 10 0.8 1 9 1 68 7 0.8 1 7 69 3 0.8 1 3 70 2 0.8 1 1 1 71 3 0.8 1 2 1 72 3 0.8 1 3 73 5 0.8 1 4 1 74 6 0.8 1 3 3 75 4 0.8 1 4 76 6 0.8 1 6 77 11 0.8 1 10 1 78 12 0.8 1 11 1 79 7 0.8 1 7 80 10 0.8 1 8 2 81 5 0.8 1 4 1 82 11 0.8 1 6 5 83 8 0.8 1 8 84 8 0.8 1 7 1 85 10 0.8 1 9 1 86 6 0.8 1 5 1 87 7 0.8 1 5 2 88 6 0.8 1 6 89 8 0.8 1 7 1 90 8 0.8 1 7 1 91 6 0.8 1 4 2 92 5 0.8 1 4 1 93 6 0.8 1 6 94 6 0.8 1 6 95 6 0.8 1 6 96 9 0.8 1 9 97 8 0.8 1 5 3 98 10 0.8 1 9 1 99 16 0.8 1 14 2 100 8 0.8 1 7 1 101 4 0.8 1 4 102 6 0.8 1 4 2 103 8 0.8 1 8 104 6 0.8 1 4 2 105 9 0.8 1 9 106 2 0.8 1 2 107 9 0.8 1 8 1 108 6 0.8 1 4 2 109 11 0.8 1 10 1 110 8 0.8 1 7 1 111 7 0.8 1 6 1 112 12 0.8 1 10 2 113 9 0.8 1 8 1 114 10 0.8 1 9 1 115 7 0.8 1 4 3 116 15 0.8 1 14 1 117 19 0.8 1 17 2 118 21 0.8 1 19 2 119 16 0.8 1 15 1 120 13 0.8 1 11 2 121 18 0.8 1 13 5 122 15 0.8 1 12 3 123 12 0.8 1 8 4 124 14 0.8 1 12 2 125 15 0.8 1 12 3 126 25 0.8 1 21 4 127 21 0.8 1 18 3 128 17 0.8 1 14 3 129 17 0.8 1 13 4 130 29 0.8 1 23 6 131 21 0.8 1 17 4 132 29 0.8 1 28 1 133 27 0.8 1 18 9 134 25 0.8 1 20 5 135 41 0.8 1 20 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.fq.gz ============================================= 51337098 sequences processed in total