SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_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_21_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1655.18 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 51,337,098 Reads with adapters: 22,250,143 (43.3%) Reads written (passing filters): 51,337,098 (100.0%) Total basepairs processed: 6,502,868,062 bp Quality-trimmed: 1,736,389 bp (0.0%) Total written (filtered): 6,475,103,537 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22250143 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.0% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19934151 12834274.5 0 19934151 2 1505115 3208568.6 0 1505115 3 442293 802142.2 0 442293 4 281742 200535.5 0 281742 5 47399 50133.9 0 47399 6 11600 12533.5 0 11600 7 8370 3133.4 0 8370 8 6041 783.3 0 6041 9 1708 195.8 0 1349 359 10 10424 49.0 1 9483 941 11 127 12.2 1 27 100 12 48 3.1 1 15 33 13 9 0.8 1 2 7 14 12 0.8 1 6 6 15 7 0.8 1 5 2 16 4 0.8 1 3 1 17 11 0.8 1 6 5 18 1 0.8 1 1 19 17 0.8 1 8 9 20 7 0.8 1 6 1 21 3 0.8 1 1 2 22 5 0.8 1 5 23 8 0.8 1 3 5 24 20 0.8 1 9 11 25 7 0.8 1 5 2 26 7 0.8 1 5 2 27 3 0.8 1 3 28 9 0.8 1 4 5 29 6 0.8 1 4 2 30 8 0.8 1 0 8 31 5 0.8 1 4 1 32 10 0.8 1 3 7 33 8 0.8 1 7 1 34 3 0.8 1 3 35 7 0.8 1 6 1 36 4 0.8 1 4 37 5 0.8 1 4 1 38 6 0.8 1 3 3 39 14 0.8 1 8 6 40 10 0.8 1 4 6 41 4 0.8 1 2 2 42 14 0.8 1 11 3 43 6 0.8 1 5 1 44 6 0.8 1 4 2 45 9 0.8 1 7 2 46 5 0.8 1 4 1 47 10 0.8 1 5 5 48 9 0.8 1 5 4 49 15 0.8 1 12 3 50 5 0.8 1 4 1 51 8 0.8 1 6 2 52 10 0.8 1 8 2 53 8 0.8 1 6 2 54 6 0.8 1 4 2 55 7 0.8 1 6 1 56 4 0.8 1 2 2 57 6 0.8 1 4 2 58 6 0.8 1 4 2 60 10 0.8 1 6 4 61 2 0.8 1 2 62 8 0.8 1 6 2 63 12 0.8 1 8 4 64 7 0.8 1 6 1 65 6 0.8 1 5 1 66 12 0.8 1 10 2 67 5 0.8 1 3 2 68 2 0.8 1 2 69 9 0.8 1 9 70 6 0.8 1 4 2 71 5 0.8 1 3 2 72 2 0.8 1 2 73 10 0.8 1 10 74 4 0.8 1 3 1 75 6 0.8 1 4 2 76 5 0.8 1 3 2 77 7 0.8 1 5 2 78 6 0.8 1 6 79 11 0.8 1 8 3 80 6 0.8 1 4 2 81 6 0.8 1 4 2 82 7 0.8 1 4 3 83 7 0.8 1 7 84 6 0.8 1 5 1 85 10 0.8 1 7 3 86 9 0.8 1 7 2 87 3 0.8 1 1 2 88 12 0.8 1 11 1 89 2 0.8 1 1 1 90 9 0.8 1 5 4 91 8 0.8 1 8 92 3 0.8 1 1 2 93 2 0.8 1 2 94 1 0.8 1 0 1 95 8 0.8 1 4 4 96 8 0.8 1 6 2 97 5 0.8 1 5 98 11 0.8 1 10 1 99 5 0.8 1 3 2 100 12 0.8 1 9 3 101 6 0.8 1 5 1 102 9 0.8 1 8 1 103 10 0.8 1 7 3 104 5 0.8 1 5 105 10 0.8 1 8 2 106 9 0.8 1 7 2 107 12 0.8 1 11 1 108 10 0.8 1 8 2 109 9 0.8 1 9 110 10 0.8 1 9 1 111 9 0.8 1 6 3 112 8 0.8 1 8 113 6 0.8 1 6 114 10 0.8 1 9 1 115 16 0.8 1 14 2 116 10 0.8 1 9 1 117 13 0.8 1 12 1 118 18 0.8 1 12 6 119 8 0.8 1 4 4 120 15 0.8 1 14 1 121 15 0.8 1 13 2 122 11 0.8 1 8 3 123 19 0.8 1 15 4 124 16 0.8 1 16 125 12 0.8 1 10 2 126 16 0.8 1 15 1 127 16 0.8 1 15 1 128 26 0.8 1 25 1 129 19 0.8 1 16 3 130 16 0.8 1 13 3 131 33 0.8 1 27 6 132 14 0.8 1 11 3 133 24 0.8 1 22 2 134 25 0.8 1 19 6 135 31 0.8 1 13 18 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R2.fq.gz ============================================= 51337098 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 51337098 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 224543 (0.44%)