SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.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/Manchester/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/Manchester/data/zr3616_1_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4579.51 s (28 µs/read; 2.13 M reads/minute). === Summary === Total reads processed: 162,780,101 Reads with adapters: 62,282,524 (38.3%) Reads written (passing filters): 162,780,101 (100.0%) Total basepairs processed: 19,464,055,669 bp Quality-trimmed: 3,949,688 bp (0.0%) Total written (filtered): 19,380,382,323 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62282524 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.9% C: 10.1% G: 7.6% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 52535873 40695025.2 0 52535873 2 6572350 10173756.3 0 6572350 3 1405861 2543439.1 0 1405861 4 1125266 635859.8 0 1125266 5 369656 158964.9 0 369656 6 90653 39741.2 0 90653 7 59410 9935.3 0 59410 8 35804 2483.8 0 35804 9 6859 621.0 0 5163 1696 10 62774 155.2 1 59511 3263 11 666 38.8 1 132 534 12 181 9.7 1 79 102 13 73 2.4 1 44 29 14 44 2.4 1 34 10 15 91 2.4 1 78 13 16 34 2.4 1 27 7 17 38 2.4 1 26 12 18 98 2.4 1 87 11 19 91 2.4 1 84 7 20 102 2.4 1 92 10 21 52 2.4 1 42 10 22 47 2.4 1 37 10 23 108 2.4 1 92 16 24 74 2.4 1 64 10 25 80 2.4 1 73 7 26 76 2.4 1 68 8 27 81 2.4 1 71 10 28 56 2.4 1 47 9 29 75 2.4 1 65 10 30 71 2.4 1 65 6 31 69 2.4 1 50 19 32 61 2.4 1 51 10 33 75 2.4 1 66 9 34 61 2.4 1 55 6 35 60 2.4 1 56 4 36 66 2.4 1 60 6 37 66 2.4 1 55 11 38 71 2.4 1 62 9 39 73 2.4 1 64 9 40 82 2.4 1 73 9 41 108 2.4 1 97 11 42 75 2.4 1 69 6 43 104 2.4 1 91 13 44 101 2.4 1 88 13 45 77 2.4 1 72 5 46 83 2.4 1 77 6 47 104 2.4 1 90 14 48 86 2.4 1 74 12 49 97 2.4 1 90 7 50 116 2.4 1 105 11 51 107 2.4 1 90 17 52 113 2.4 1 104 9 53 90 2.4 1 74 16 54 112 2.4 1 94 18 55 111 2.4 1 99 12 56 106 2.4 1 96 10 57 108 2.4 1 98 10 58 87 2.4 1 77 10 59 132 2.4 1 123 9 60 132 2.4 1 111 21 61 102 2.4 1 91 11 62 103 2.4 1 93 10 63 105 2.4 1 86 19 64 86 2.4 1 76 10 65 121 2.4 1 117 4 66 130 2.4 1 115 15 67 109 2.4 1 93 16 68 119 2.4 1 104 15 69 124 2.4 1 108 16 70 139 2.4 1 123 16 71 131 2.4 1 125 6 72 112 2.4 1 99 13 73 136 2.4 1 126 10 74 156 2.4 1 136 20 75 165 2.4 1 152 13 76 146 2.4 1 127 19 77 109 2.4 1 96 13 78 145 2.4 1 125 20 79 129 2.4 1 115 14 80 156 2.4 1 142 14 81 149 2.4 1 134 15 82 124 2.4 1 110 14 83 136 2.4 1 114 22 84 121 2.4 1 109 12 85 168 2.4 1 152 16 86 141 2.4 1 125 16 87 132 2.4 1 118 14 88 155 2.4 1 144 11 89 157 2.4 1 139 18 90 152 2.4 1 137 15 91 139 2.4 1 126 13 92 143 2.4 1 130 13 93 147 2.4 1 131 16 94 131 2.4 1 117 14 95 155 2.4 1 130 25 96 125 2.4 1 107 18 97 161 2.4 1 146 15 98 146 2.4 1 135 11 99 158 2.4 1 145 13 100 132 2.4 1 123 9 101 180 2.4 1 152 28 102 140 2.4 1 131 9 103 136 2.4 1 122 14 104 150 2.4 1 140 10 105 139 2.4 1 122 17 106 173 2.4 1 149 24 107 161 2.4 1 137 24 108 200 2.4 1 179 21 109 183 2.4 1 161 22 110 200 2.4 1 177 23 111 176 2.4 1 162 14 112 160 2.4 1 143 17 113 192 2.4 1 168 24 114 223 2.4 1 203 20 115 202 2.4 1 179 23 116 220 2.4 1 193 27 117 193 2.4 1 173 20 118 244 2.4 1 223 21 119 198 2.4 1 177 21 120 198 2.4 1 177 21 121 206 2.4 1 182 24 122 204 2.4 1 178 26 123 227 2.4 1 193 34 124 221 2.4 1 199 22 125 210 2.4 1 181 29 126 211 2.4 1 189 22 127 230 2.4 1 209 21 128 274 2.4 1 250 24 129 283 2.4 1 254 29 130 293 2.4 1 275 18 131 284 2.4 1 250 34 132 331 2.4 1 292 39 133 362 2.4 1 305 57 134 296 2.4 1 223 73 135 452 2.4 1 194 258 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.fq.gz ============================================= 162780101 sequences processed in total