SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_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_23_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1318.67 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 40,743,756 Reads with adapters: 17,351,768 (42.6%) Reads written (passing filters): 40,743,756 (100.0%) Total basepairs processed: 5,120,592,948 bp Quality-trimmed: 1,710,015 bp (0.0%) Total written (filtered): 5,098,406,294 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17351768 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15448638 10185939.0 0 15448638 2 1237821 2546484.8 0 1237821 3 352171 636621.2 0 352171 4 234395 159155.3 0 234395 5 42680 39788.8 0 42680 6 10437 9947.2 0 10437 7 7966 2486.8 0 7966 8 5733 621.7 0 5733 9 1586 155.4 0 1253 333 10 9480 38.9 1 8647 833 11 83 9.7 1 10 73 12 28 2.4 1 6 22 13 3 0.6 1 1 2 14 5 0.6 1 1 4 15 2 0.6 1 1 1 16 3 0.6 1 1 2 17 4 0.6 1 1 3 19 2 0.6 1 0 2 20 4 0.6 1 2 2 21 3 0.6 1 3 22 5 0.6 1 5 23 5 0.6 1 2 3 24 5 0.6 1 0 5 25 2 0.6 1 2 27 3 0.6 1 2 1 28 4 0.6 1 3 1 29 4 0.6 1 3 1 30 5 0.6 1 5 31 4 0.6 1 2 2 32 2 0.6 1 2 33 2 0.6 1 1 1 34 3 0.6 1 1 2 35 5 0.6 1 4 1 38 2 0.6 1 2 39 3 0.6 1 1 2 40 4 0.6 1 3 1 41 4 0.6 1 4 42 3 0.6 1 3 43 5 0.6 1 4 1 44 5 0.6 1 2 3 45 5 0.6 1 2 3 46 6 0.6 1 3 3 47 5 0.6 1 3 2 48 2 0.6 1 2 49 5 0.6 1 4 1 50 3 0.6 1 3 51 4 0.6 1 3 1 52 1 0.6 1 1 53 4 0.6 1 2 2 54 1 0.6 1 0 1 55 7 0.6 1 5 2 56 3 0.6 1 2 1 57 5 0.6 1 1 4 58 7 0.6 1 4 3 59 5 0.6 1 5 60 4 0.6 1 3 1 61 4 0.6 1 4 62 4 0.6 1 2 2 63 2 0.6 1 1 1 64 2 0.6 1 2 65 9 0.6 1 8 1 66 4 0.6 1 0 4 67 1 0.6 1 1 68 5 0.6 1 4 1 69 4 0.6 1 3 1 70 6 0.6 1 5 1 71 6 0.6 1 3 3 72 3 0.6 1 2 1 73 6 0.6 1 4 2 74 3 0.6 1 2 1 75 2 0.6 1 2 76 2 0.6 1 1 1 77 3 0.6 1 2 1 78 3 0.6 1 2 1 79 5 0.6 1 4 1 80 3 0.6 1 3 81 6 0.6 1 4 2 82 7 0.6 1 7 83 6 0.6 1 4 2 84 1 0.6 1 1 85 3 0.6 1 2 1 86 5 0.6 1 3 2 87 3 0.6 1 3 88 5 0.6 1 4 1 89 5 0.6 1 4 1 90 5 0.6 1 4 1 91 2 0.6 1 1 1 92 3 0.6 1 3 93 1 0.6 1 1 94 3 0.6 1 2 1 95 2 0.6 1 1 1 96 4 0.6 1 3 1 97 10 0.6 1 6 4 98 12 0.6 1 11 1 99 12 0.6 1 11 1 100 11 0.6 1 7 4 101 7 0.6 1 6 1 102 9 0.6 1 8 1 103 4 0.6 1 1 3 104 6 0.6 1 3 3 105 4 0.6 1 2 2 106 4 0.6 1 3 1 107 6 0.6 1 3 3 108 3 0.6 1 3 109 5 0.6 1 4 1 110 7 0.6 1 6 1 111 7 0.6 1 6 1 112 10 0.6 1 9 1 113 4 0.6 1 3 1 114 10 0.6 1 10 115 9 0.6 1 5 4 116 12 0.6 1 9 3 117 15 0.6 1 12 3 118 12 0.6 1 12 119 9 0.6 1 7 2 120 19 0.6 1 17 2 121 13 0.6 1 12 1 122 17 0.6 1 15 2 123 9 0.6 1 9 124 20 0.6 1 19 1 125 8 0.6 1 8 126 14 0.6 1 11 3 127 14 0.6 1 9 5 128 12 0.6 1 11 1 129 20 0.6 1 15 5 130 21 0.6 1 18 3 131 14 0.6 1 12 2 132 16 0.6 1 15 1 133 19 0.6 1 17 2 134 17 0.6 1 11 6 135 23 0.6 1 10 13 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R2.fq.gz ============================================= 40743756 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 40743756 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 204735 (0.50%)