SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_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_9_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1528.07 s (31 µs/read; 1.93 M reads/minute). === Summary === Total reads processed: 49,101,606 Reads with adapters: 20,209,348 (41.2%) Reads written (passing filters): 49,101,606 (100.0%) Total basepairs processed: 6,079,740,279 bp Quality-trimmed: 1,919,505 bp (0.0%) Total written (filtered): 6,053,388,645 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20209348 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.8% C: 10.1% G: 6.8% T: 38.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17670933 12275401.5 0 17670933 2 1676774 3068850.4 0 1676774 3 435504 767212.6 0 435504 4 294070 191803.1 0 294070 5 71211 47950.8 0 71211 6 17963 11987.7 0 17963 7 13193 2996.9 0 13193 8 9913 749.2 0 9913 9 2386 187.3 0 1891 495 10 15816 46.8 1 14684 1132 11 180 11.7 1 37 143 12 79 2.9 1 24 55 13 11 0.7 1 2 9 14 21 0.7 1 9 12 15 3 0.7 1 1 2 16 16 0.7 1 9 7 17 2 0.7 1 0 2 18 28 0.7 1 13 15 19 35 0.7 1 25 10 20 2 0.7 1 1 1 21 3 0.7 1 3 22 7 0.7 1 5 2 23 13 0.7 1 10 3 24 19 0.7 1 12 7 25 1 0.7 1 1 26 12 0.7 1 8 4 27 14 0.7 1 8 6 28 8 0.7 1 5 3 29 7 0.7 1 7 30 16 0.7 1 11 5 31 18 0.7 1 11 7 32 3 0.7 1 1 2 33 19 0.7 1 15 4 34 3 0.7 1 3 35 14 0.7 1 11 3 36 8 0.7 1 4 4 37 15 0.7 1 12 3 38 7 0.7 1 5 2 39 9 0.7 1 7 2 40 11 0.7 1 8 3 41 15 0.7 1 12 3 42 12 0.7 1 9 3 43 10 0.7 1 8 2 44 11 0.7 1 9 2 45 2 0.7 1 1 1 46 2 0.7 1 0 2 47 5 0.7 1 2 3 48 14 0.7 1 9 5 49 7 0.7 1 4 3 50 8 0.7 1 7 1 51 14 0.7 1 9 5 52 11 0.7 1 8 3 53 5 0.7 1 4 1 54 2 0.7 1 2 55 12 0.7 1 10 2 56 14 0.7 1 12 2 57 4 0.7 1 3 1 58 4 0.7 1 3 1 59 6 0.7 1 5 1 60 4 0.7 1 3 1 61 8 0.7 1 4 4 62 9 0.7 1 7 2 63 3 0.7 1 3 64 5 0.7 1 4 1 65 6 0.7 1 5 1 66 17 0.7 1 14 3 67 4 0.7 1 4 68 9 0.7 1 9 69 6 0.7 1 6 70 6 0.7 1 5 1 71 4 0.7 1 4 72 8 0.7 1 5 3 73 4 0.7 1 4 74 8 0.7 1 8 75 4 0.7 1 4 76 9 0.7 1 7 2 77 11 0.7 1 9 2 78 4 0.7 1 3 1 79 7 0.7 1 5 2 80 9 0.7 1 7 2 81 5 0.7 1 5 82 8 0.7 1 5 3 83 7 0.7 1 6 1 84 6 0.7 1 2 4 85 4 0.7 1 3 1 86 7 0.7 1 7 87 4 0.7 1 4 88 7 0.7 1 7 89 4 0.7 1 2 2 90 4 0.7 1 3 1 91 7 0.7 1 5 2 92 12 0.7 1 8 4 93 10 0.7 1 5 5 94 10 0.7 1 10 95 2 0.7 1 2 96 11 0.7 1 11 97 10 0.7 1 8 2 98 6 0.7 1 3 3 99 10 0.7 1 10 100 14 0.7 1 13 1 101 4 0.7 1 4 102 13 0.7 1 9 4 103 9 0.7 1 8 1 104 8 0.7 1 6 2 105 11 0.7 1 8 3 106 14 0.7 1 14 107 7 0.7 1 6 1 108 13 0.7 1 12 1 109 7 0.7 1 4 3 110 9 0.7 1 7 2 111 14 0.7 1 14 112 11 0.7 1 10 1 113 11 0.7 1 11 114 9 0.7 1 8 1 115 11 0.7 1 8 3 116 13 0.7 1 10 3 117 13 0.7 1 11 2 118 12 0.7 1 12 119 13 0.7 1 12 1 120 17 0.7 1 15 2 121 17 0.7 1 15 2 122 19 0.7 1 11 8 123 16 0.7 1 13 3 124 34 0.7 1 33 1 125 14 0.7 1 10 4 126 19 0.7 1 12 7 127 22 0.7 1 19 3 128 22 0.7 1 17 5 129 20 0.7 1 14 6 130 24 0.7 1 23 1 131 18 0.7 1 17 1 132 24 0.7 1 19 5 133 24 0.7 1 23 1 134 25 0.7 1 18 7 135 33 0.7 1 8 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R1.fq.gz ============================================= 49101606 sequences processed in total