SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_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_4_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5518.47 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 199,920,896 Reads with adapters: 74,214,434 (37.1%) Reads written (passing filters): 199,920,896 (100.0%) Total basepairs processed: 23,462,606,601 bp Quality-trimmed: 5,081,221 bp (0.0%) Total written (filtered): 23,360,095,022 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74214434 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.8% G: 7.9% T: 39.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 61435800 49980224.0 0 61435800 2 8622690 12495056.0 0 8622690 3 1721129 3123764.0 0 1721129 4 1486347 780941.0 0 1486347 5 522326 195235.2 0 522326 6 133103 48808.8 0 133103 7 92467 12202.2 0 92467 8 60243 3050.6 0 60243 9 11091 762.6 0 8625 2466 10 105760 190.7 1 101028 4732 11 1009 47.7 1 203 806 12 316 11.9 1 140 176 13 69 3.0 1 42 27 14 66 3.0 1 55 11 15 126 3.0 1 113 13 16 33 3.0 1 27 6 17 47 3.0 1 35 12 18 127 3.0 1 111 16 19 105 3.0 1 95 10 20 146 3.0 1 121 25 21 77 3.0 1 67 10 22 57 3.0 1 49 8 23 175 3.0 1 161 14 24 92 3.0 1 83 9 25 109 3.0 1 96 13 26 89 3.0 1 80 9 27 114 3.0 1 95 19 28 83 3.0 1 79 4 29 72 3.0 1 64 8 30 99 3.0 1 82 17 31 81 3.0 1 67 14 32 101 3.0 1 89 12 33 89 3.0 1 82 7 34 100 3.0 1 88 12 35 99 3.0 1 85 14 36 95 3.0 1 84 11 37 102 3.0 1 90 12 38 110 3.0 1 97 13 39 105 3.0 1 94 11 40 95 3.0 1 77 18 41 126 3.0 1 114 12 42 110 3.0 1 95 15 43 112 3.0 1 104 8 44 122 3.0 1 110 12 45 110 3.0 1 98 12 46 140 3.0 1 126 14 47 147 3.0 1 137 10 48 154 3.0 1 134 20 49 115 3.0 1 95 20 50 148 3.0 1 129 19 51 139 3.0 1 120 19 52 118 3.0 1 102 16 53 137 3.0 1 123 14 54 140 3.0 1 127 13 55 154 3.0 1 135 19 56 147 3.0 1 132 15 57 134 3.0 1 116 18 58 155 3.0 1 138 17 59 172 3.0 1 155 17 60 152 3.0 1 142 10 61 178 3.0 1 164 14 62 177 3.0 1 162 15 63 141 3.0 1 131 10 64 152 3.0 1 129 23 65 150 3.0 1 142 8 66 182 3.0 1 156 26 67 192 3.0 1 173 19 68 189 3.0 1 170 19 69 156 3.0 1 134 22 70 191 3.0 1 174 17 71 189 3.0 1 170 19 72 178 3.0 1 167 11 73 194 3.0 1 178 16 74 192 3.0 1 176 16 75 174 3.0 1 156 18 76 176 3.0 1 156 20 77 173 3.0 1 159 14 78 191 3.0 1 164 27 79 207 3.0 1 193 14 80 187 3.0 1 165 22 81 189 3.0 1 169 20 82 187 3.0 1 171 16 83 196 3.0 1 178 18 84 198 3.0 1 182 16 85 181 3.0 1 154 27 86 214 3.0 1 186 28 87 181 3.0 1 163 18 88 207 3.0 1 180 27 89 183 3.0 1 169 14 90 194 3.0 1 173 21 91 210 3.0 1 192 18 92 204 3.0 1 181 23 93 174 3.0 1 159 15 94 170 3.0 1 150 20 95 224 3.0 1 193 31 96 188 3.0 1 166 22 97 199 3.0 1 168 31 98 241 3.0 1 223 18 99 230 3.0 1 205 25 100 212 3.0 1 190 22 101 223 3.0 1 199 24 102 216 3.0 1 192 24 103 211 3.0 1 192 19 104 200 3.0 1 179 21 105 185 3.0 1 163 22 106 227 3.0 1 198 29 107 235 3.0 1 210 25 108 219 3.0 1 190 29 109 235 3.0 1 201 34 110 224 3.0 1 191 33 111 225 3.0 1 190 35 112 222 3.0 1 201 21 113 209 3.0 1 194 15 114 229 3.0 1 193 36 115 236 3.0 1 209 27 116 239 3.0 1 217 22 117 242 3.0 1 210 32 118 245 3.0 1 229 16 119 258 3.0 1 237 21 120 266 3.0 1 236 30 121 236 3.0 1 202 34 122 269 3.0 1 233 36 123 272 3.0 1 246 26 124 260 3.0 1 239 21 125 270 3.0 1 240 30 126 294 3.0 1 263 31 127 298 3.0 1 267 31 128 305 3.0 1 261 44 129 307 3.0 1 278 29 130 294 3.0 1 262 32 131 295 3.0 1 255 40 132 344 3.0 1 313 31 133 384 3.0 1 326 58 134 335 3.0 1 227 108 135 498 3.0 1 245 253 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R1.fq.gz ============================================= 199920896 sequences processed in total