SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_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_3_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1300.37 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 39,620,531 Reads with adapters: 17,150,562 (43.3%) Reads written (passing filters): 39,620,531 (100.0%) Total basepairs processed: 5,015,593,115 bp Quality-trimmed: 1,602,642 bp (0.0%) Total written (filtered): 4,993,811,589 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17150562 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.2% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15315313 9905132.8 0 15315313 2 1190584 2476283.2 0 1190584 3 348180 619070.8 0 348180 4 222979 154767.7 0 222979 5 38963 38691.9 0 38963 6 9791 9673.0 0 9791 7 7052 2418.2 0 7052 8 5372 604.6 0 5372 9 1533 151.1 0 1257 276 10 9668 37.8 1 8907 761 11 121 9.4 1 16 105 12 32 2.4 1 6 26 13 4 0.6 1 1 3 14 6 0.6 1 1 5 15 8 0.6 1 7 1 16 3 0.6 1 2 1 17 3 0.6 1 2 1 18 3 0.6 1 2 1 19 9 0.6 1 3 6 20 4 0.6 1 3 1 21 5 0.6 1 3 2 22 2 0.6 1 0 2 23 3 0.6 1 1 2 24 9 0.6 1 5 4 25 1 0.6 1 0 1 26 3 0.6 1 1 2 27 1 0.6 1 1 28 6 0.6 1 4 2 29 7 0.6 1 4 3 30 6 0.6 1 5 1 31 9 0.6 1 6 3 32 9 0.6 1 6 3 33 6 0.6 1 6 34 3 0.6 1 2 1 35 12 0.6 1 11 1 36 6 0.6 1 4 2 37 4 0.6 1 4 38 5 0.6 1 5 39 3 0.6 1 2 1 40 10 0.6 1 7 3 41 4 0.6 1 3 1 42 4 0.6 1 3 1 43 7 0.6 1 6 1 44 10 0.6 1 6 4 45 11 0.6 1 5 6 46 9 0.6 1 8 1 47 7 0.6 1 4 3 48 3 0.6 1 1 2 49 5 0.6 1 1 4 50 8 0.6 1 4 4 51 4 0.6 1 4 52 3 0.6 1 3 53 7 0.6 1 6 1 54 5 0.6 1 2 3 55 6 0.6 1 4 2 56 4 0.6 1 2 2 57 7 0.6 1 4 3 58 5 0.6 1 4 1 59 4 0.6 1 3 1 60 3 0.6 1 3 62 5 0.6 1 2 3 63 1 0.6 1 1 64 2 0.6 1 1 1 65 6 0.6 1 4 2 66 2 0.6 1 1 1 67 4 0.6 1 3 1 68 4 0.6 1 4 69 2 0.6 1 2 70 2 0.6 1 2 71 4 0.6 1 3 1 72 2 0.6 1 1 1 73 6 0.6 1 5 1 74 8 0.6 1 6 2 75 6 0.6 1 5 1 76 9 0.6 1 6 3 77 5 0.6 1 4 1 78 4 0.6 1 3 1 79 7 0.6 1 2 5 80 4 0.6 1 3 1 81 5 0.6 1 3 2 82 7 0.6 1 4 3 83 12 0.6 1 10 2 84 3 0.6 1 3 85 6 0.6 1 6 86 7 0.6 1 6 1 87 8 0.6 1 6 2 88 7 0.6 1 5 2 89 6 0.6 1 6 90 7 0.6 1 6 1 91 7 0.6 1 6 1 92 5 0.6 1 5 93 10 0.6 1 10 94 7 0.6 1 6 1 95 5 0.6 1 4 1 96 10 0.6 1 6 4 97 6 0.6 1 4 2 98 10 0.6 1 9 1 99 9 0.6 1 7 2 100 10 0.6 1 9 1 101 3 0.6 1 2 1 102 10 0.6 1 8 2 103 4 0.6 1 3 1 104 8 0.6 1 7 1 105 9 0.6 1 9 106 7 0.6 1 7 107 11 0.6 1 9 2 108 6 0.6 1 6 109 9 0.6 1 7 2 110 12 0.6 1 4 8 111 13 0.6 1 10 3 112 3 0.6 1 2 1 113 7 0.6 1 6 1 114 10 0.6 1 7 3 115 16 0.6 1 15 1 116 10 0.6 1 8 2 117 9 0.6 1 8 1 118 11 0.6 1 9 2 119 14 0.6 1 12 2 120 8 0.6 1 8 121 15 0.6 1 14 1 122 17 0.6 1 17 123 15 0.6 1 10 5 124 13 0.6 1 11 2 125 11 0.6 1 9 2 126 12 0.6 1 9 3 127 17 0.6 1 14 3 128 24 0.6 1 21 3 129 24 0.6 1 21 3 130 17 0.6 1 12 5 131 21 0.6 1 20 1 132 25 0.6 1 21 4 133 20 0.6 1 16 4 134 23 0.6 1 16 7 135 44 0.6 1 16 28 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R2.fq.gz ============================================= 39620531 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 39620531 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 173910 (0.44%)