SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_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_14_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1183.34 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 37,045,803 Reads with adapters: 15,901,700 (42.9%) Reads written (passing filters): 37,045,803 (100.0%) Total basepairs processed: 4,677,677,552 bp Quality-trimmed: 1,158,321 bp (0.0%) Total written (filtered): 4,657,794,991 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15901700 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.1% G: 6.2% T: 38.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14192161 9261450.8 0 14192161 2 1108291 2315362.7 0 1108291 3 317814 578840.7 0 317814 4 209516 144710.2 0 209516 5 40045 36177.5 0 40045 6 9813 9044.4 0 9813 7 7173 2261.1 0 7173 8 5447 565.3 0 5447 9 1388 141.3 0 1097 291 10 9275 35.3 1 8582 693 11 112 8.8 1 17 95 12 20 2.2 1 7 13 13 3 0.6 1 0 3 14 2 0.6 1 0 2 16 3 0.6 1 1 2 17 2 0.6 1 2 18 1 0.6 1 0 1 19 3 0.6 1 0 3 21 2 0.6 1 1 1 22 1 0.6 1 1 23 2 0.6 1 1 1 24 1 0.6 1 1 25 1 0.6 1 1 26 2 0.6 1 1 1 27 3 0.6 1 3 29 1 0.6 1 0 1 30 2 0.6 1 1 1 31 2 0.6 1 1 1 32 6 0.6 1 4 2 33 6 0.6 1 4 2 34 2 0.6 1 1 1 35 3 0.6 1 3 37 1 0.6 1 1 38 1 0.6 1 1 39 2 0.6 1 2 40 1 0.6 1 0 1 41 1 0.6 1 1 42 2 0.6 1 2 43 3 0.6 1 1 2 45 2 0.6 1 2 46 2 0.6 1 1 1 47 1 0.6 1 0 1 48 4 0.6 1 2 2 49 3 0.6 1 2 1 51 3 0.6 1 3 52 2 0.6 1 2 53 4 0.6 1 4 54 3 0.6 1 3 55 4 0.6 1 3 1 56 2 0.6 1 2 57 4 0.6 1 3 1 58 3 0.6 1 2 1 59 1 0.6 1 0 1 60 7 0.6 1 5 2 61 3 0.6 1 2 1 62 3 0.6 1 2 1 63 8 0.6 1 6 2 64 5 0.6 1 4 1 65 2 0.6 1 2 66 1 0.6 1 1 67 3 0.6 1 3 68 1 0.6 1 1 70 1 0.6 1 1 71 3 0.6 1 3 72 4 0.6 1 3 1 73 3 0.6 1 1 2 74 2 0.6 1 2 75 4 0.6 1 3 1 76 1 0.6 1 0 1 77 2 0.6 1 2 78 6 0.6 1 5 1 79 3 0.6 1 3 80 6 0.6 1 5 1 81 3 0.6 1 3 82 5 0.6 1 5 83 2 0.6 1 1 1 84 2 0.6 1 2 85 3 0.6 1 2 1 86 7 0.6 1 6 1 87 2 0.6 1 2 88 8 0.6 1 6 2 89 8 0.6 1 8 90 3 0.6 1 3 91 4 0.6 1 4 92 4 0.6 1 4 93 9 0.6 1 5 4 94 2 0.6 1 2 95 3 0.6 1 3 96 1 0.6 1 1 97 5 0.6 1 2 3 98 7 0.6 1 6 1 99 6 0.6 1 6 100 7 0.6 1 6 1 101 7 0.6 1 5 2 102 2 0.6 1 1 1 103 3 0.6 1 3 104 6 0.6 1 5 1 105 5 0.6 1 4 1 106 5 0.6 1 5 107 7 0.6 1 7 108 3 0.6 1 3 109 6 0.6 1 5 1 110 5 0.6 1 4 1 111 5 0.6 1 5 112 10 0.6 1 10 113 10 0.6 1 10 114 7 0.6 1 7 115 15 0.6 1 13 2 116 11 0.6 1 9 2 117 7 0.6 1 7 118 11 0.6 1 9 2 119 16 0.6 1 16 120 12 0.6 1 11 1 121 9 0.6 1 8 1 122 14 0.6 1 13 1 123 15 0.6 1 13 2 124 7 0.6 1 5 2 125 9 0.6 1 6 3 126 13 0.6 1 13 127 19 0.6 1 17 2 128 17 0.6 1 13 4 129 20 0.6 1 16 4 130 23 0.6 1 21 2 131 10 0.6 1 9 1 132 20 0.6 1 17 3 133 14 0.6 1 11 3 134 15 0.6 1 11 4 135 31 0.6 1 16 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R2.fq.gz ============================================= 37045803 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 37045803 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 174047 (0.47%)