SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_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_12_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1548.34 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 47,871,006 Reads with adapters: 20,525,648 (42.9%) Reads written (passing filters): 47,871,006 (100.0%) Total basepairs processed: 6,042,854,501 bp Quality-trimmed: 1,702,355 bp (0.0%) Total written (filtered): 6,017,085,430 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20525648 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 9.9% G: 5.8% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18406616 11967751.5 0 18406616 2 1361487 2991937.9 0 1361487 3 391002 747984.5 0 391002 4 266858 186996.1 0 266858 5 55111 46749.0 0 55111 6 13358 11687.3 0 13358 7 9112 2921.8 0 9112 8 6597 730.5 0 6597 9 2003 182.6 0 1676 327 10 12450 45.7 1 11470 980 11 128 11.4 1 23 105 12 41 2.9 1 10 31 13 12 0.7 1 3 9 14 6 0.7 1 1 5 15 6 0.7 1 3 3 16 1 0.7 1 1 17 6 0.7 1 3 3 18 2 0.7 1 0 2 19 9 0.7 1 6 3 20 5 0.7 1 3 2 21 4 0.7 1 3 1 22 7 0.7 1 6 1 23 1 0.7 1 0 1 24 9 0.7 1 4 5 25 4 0.7 1 3 1 26 3 0.7 1 3 27 4 0.7 1 0 4 28 4 0.7 1 2 2 29 2 0.7 1 2 30 6 0.7 1 5 1 31 1 0.7 1 0 1 32 9 0.7 1 6 3 33 3 0.7 1 2 1 34 3 0.7 1 3 35 6 0.7 1 2 4 36 5 0.7 1 2 3 37 7 0.7 1 5 2 38 4 0.7 1 2 2 39 5 0.7 1 3 2 40 5 0.7 1 4 1 41 2 0.7 1 1 1 42 5 0.7 1 3 2 43 4 0.7 1 3 1 44 5 0.7 1 4 1 45 6 0.7 1 5 1 46 1 0.7 1 1 47 7 0.7 1 5 2 48 6 0.7 1 4 2 49 5 0.7 1 4 1 50 4 0.7 1 3 1 51 2 0.7 1 2 52 4 0.7 1 3 1 53 7 0.7 1 4 3 54 6 0.7 1 4 2 55 7 0.7 1 6 1 56 5 0.7 1 4 1 57 6 0.7 1 2 4 58 5 0.7 1 3 2 59 1 0.7 1 0 1 60 12 0.7 1 8 4 61 2 0.7 1 2 62 2 0.7 1 2 63 6 0.7 1 5 1 64 1 0.7 1 1 65 3 0.7 1 1 2 66 13 0.7 1 12 1 67 3 0.7 1 3 68 5 0.7 1 2 3 69 3 0.7 1 2 1 70 3 0.7 1 3 71 1 0.7 1 0 1 72 3 0.7 1 3 73 1 0.7 1 1 74 4 0.7 1 3 1 75 6 0.7 1 4 2 76 7 0.7 1 5 2 77 7 0.7 1 2 5 78 4 0.7 1 4 79 4 0.7 1 4 80 7 0.7 1 5 2 81 1 0.7 1 0 1 82 3 0.7 1 2 1 83 4 0.7 1 2 2 84 6 0.7 1 4 2 85 8 0.7 1 8 86 6 0.7 1 6 87 2 0.7 1 2 88 3 0.7 1 3 89 3 0.7 1 3 90 4 0.7 1 2 2 91 4 0.7 1 3 1 92 5 0.7 1 3 2 93 6 0.7 1 4 2 94 3 0.7 1 3 95 3 0.7 1 3 96 13 0.7 1 10 3 97 13 0.7 1 11 2 98 4 0.7 1 3 1 99 6 0.7 1 4 2 100 7 0.7 1 4 3 101 6 0.7 1 6 102 7 0.7 1 6 1 103 5 0.7 1 2 3 104 9 0.7 1 7 2 105 7 0.7 1 5 2 106 8 0.7 1 8 107 8 0.7 1 7 1 108 7 0.7 1 6 1 109 9 0.7 1 9 110 9 0.7 1 9 111 4 0.7 1 3 1 112 5 0.7 1 5 113 13 0.7 1 11 2 114 7 0.7 1 7 115 16 0.7 1 16 116 16 0.7 1 15 1 117 25 0.7 1 22 3 118 11 0.7 1 10 1 119 24 0.7 1 22 2 120 9 0.7 1 8 1 121 14 0.7 1 13 1 122 10 0.7 1 8 2 123 13 0.7 1 11 2 124 11 0.7 1 8 3 125 13 0.7 1 10 3 126 10 0.7 1 9 1 127 14 0.7 1 14 128 10 0.7 1 9 1 129 25 0.7 1 22 3 130 13 0.7 1 10 3 131 15 0.7 1 14 1 132 33 0.7 1 26 7 133 24 0.7 1 22 2 134 17 0.7 1 10 7 135 30 0.7 1 13 17 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R2.fq.gz ============================================= 47871006 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 47871006 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 198066 (0.41%)