SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_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_2_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1826.49 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 55,879,313 Reads with adapters: 24,629,147 (44.1%) Reads written (passing filters): 55,879,313 (100.0%) Total basepairs processed: 7,129,414,230 bp Quality-trimmed: 2,033,369 bp (0.0%) Total written (filtered): 7,098,489,333 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24629147 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.4% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21978299 13969828.2 0 21978299 2 1758396 3492457.1 0 1758396 3 499911 873114.3 0 499911 4 296834 218278.6 0 296834 5 49700 54569.6 0 49700 6 12916 13642.4 0 12916 7 9268 3410.6 0 9268 8 6943 852.7 0 6943 9 1916 213.2 0 1464 452 10 13264 53.3 1 12169 1095 11 183 13.3 1 31 152 12 82 3.3 1 20 62 13 15 0.8 1 3 12 14 29 0.8 1 20 9 15 3 0.8 1 2 1 16 23 0.8 1 15 8 17 5 0.8 1 1 4 18 25 0.8 1 17 8 19 33 0.8 1 24 9 20 2 0.8 1 0 2 21 9 0.8 1 4 5 22 4 0.8 1 3 1 23 25 0.8 1 15 10 24 26 0.8 1 14 12 25 5 0.8 1 3 2 26 10 0.8 1 7 3 27 11 0.8 1 9 2 28 2 0.8 1 1 1 29 9 0.8 1 6 3 30 20 0.8 1 12 8 31 23 0.8 1 14 9 32 6 0.8 1 4 2 33 23 0.8 1 22 1 34 9 0.8 1 4 5 35 8 0.8 1 6 2 36 14 0.8 1 12 2 37 12 0.8 1 7 5 38 22 0.8 1 16 6 39 14 0.8 1 12 2 40 11 0.8 1 10 1 41 14 0.8 1 10 4 42 8 0.8 1 5 3 43 17 0.8 1 15 2 44 20 0.8 1 17 3 45 2 0.8 1 0 2 46 6 0.8 1 2 4 47 3 0.8 1 2 1 48 23 0.8 1 19 4 49 15 0.8 1 10 5 50 4 0.8 1 2 2 51 8 0.8 1 6 2 52 16 0.8 1 14 2 53 2 0.8 1 1 1 54 2 0.8 1 2 55 16 0.8 1 12 4 56 14 0.8 1 12 2 57 4 0.8 1 2 2 58 9 0.8 1 8 1 59 12 0.8 1 8 4 60 10 0.8 1 9 1 61 8 0.8 1 8 62 11 0.8 1 9 2 63 6 0.8 1 4 2 64 8 0.8 1 4 4 65 8 0.8 1 8 66 7 0.8 1 6 1 67 7 0.8 1 7 68 9 0.8 1 6 3 69 6 0.8 1 3 3 70 3 0.8 1 2 1 71 7 0.8 1 7 72 3 0.8 1 0 3 73 5 0.8 1 4 1 74 9 0.8 1 7 2 75 5 0.8 1 5 76 4 0.8 1 2 2 77 9 0.8 1 7 2 78 7 0.8 1 5 2 79 8 0.8 1 7 1 80 6 0.8 1 4 2 81 13 0.8 1 11 2 82 6 0.8 1 6 83 6 0.8 1 4 2 84 6 0.8 1 4 2 85 5 0.8 1 5 86 8 0.8 1 4 4 87 7 0.8 1 6 1 88 11 0.8 1 10 1 89 4 0.8 1 4 90 8 0.8 1 6 2 91 8 0.8 1 6 2 92 9 0.8 1 7 2 93 11 0.8 1 7 4 94 6 0.8 1 4 2 95 6 0.8 1 3 3 96 9 0.8 1 8 1 97 10 0.8 1 7 3 98 3 0.8 1 3 99 9 0.8 1 9 100 6 0.8 1 4 2 101 6 0.8 1 5 1 102 9 0.8 1 6 3 103 6 0.8 1 4 2 104 10 0.8 1 8 2 105 20 0.8 1 16 4 106 7 0.8 1 5 2 107 13 0.8 1 13 108 13 0.8 1 8 5 109 8 0.8 1 7 1 110 7 0.8 1 6 1 111 13 0.8 1 11 2 112 14 0.8 1 12 2 113 10 0.8 1 9 1 114 9 0.8 1 6 3 115 13 0.8 1 11 2 116 18 0.8 1 15 3 117 13 0.8 1 11 2 118 16 0.8 1 13 3 119 12 0.8 1 12 120 18 0.8 1 17 1 121 14 0.8 1 12 2 122 8 0.8 1 6 2 123 14 0.8 1 12 2 124 17 0.8 1 15 2 125 12 0.8 1 10 2 126 19 0.8 1 18 1 127 14 0.8 1 13 1 128 23 0.8 1 23 129 24 0.8 1 22 2 130 16 0.8 1 16 131 21 0.8 1 20 1 132 31 0.8 1 24 7 133 29 0.8 1 20 9 134 29 0.8 1 23 6 135 39 0.8 1 17 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R1.fq.gz ============================================= 55879313 sequences processed in total