SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_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/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_8_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4610.64 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 163,170,949 Reads with adapters: 60,258,226 (36.9%) Reads written (passing filters): 163,170,949 (100.0%) Total basepairs processed: 19,053,229,657 bp Quality-trimmed: 4,238,850 bp (0.0%) Total written (filtered): 18,970,596,628 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60258226 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.5% C: 9.7% G: 7.7% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 50222130 40792737.2 0 50222130 2 6829661 10198184.3 0 6829661 3 1365339 2549546.1 0 1365339 4 1200059 637386.5 0 1200059 5 369955 159346.6 0 369955 6 88415 39836.7 0 88415 7 62111 9959.2 0 62111 8 39241 2489.8 0 39241 9 6798 622.4 0 5105 1693 10 51956 155.6 1 48511 3445 11 579 38.9 1 108 471 12 192 9.7 1 119 73 13 142 2.4 1 126 16 14 50 2.4 1 38 12 15 149 2.4 1 128 21 16 42 2.4 1 33 9 17 62 2.4 1 51 11 18 101 2.4 1 89 12 19 109 2.4 1 86 23 20 124 2.4 1 109 15 21 67 2.4 1 57 10 22 68 2.4 1 58 10 23 130 2.4 1 117 13 24 86 2.4 1 73 13 25 112 2.4 1 98 14 26 67 2.4 1 57 10 27 92 2.4 1 81 11 28 75 2.4 1 65 10 29 93 2.4 1 81 12 30 78 2.4 1 71 7 31 98 2.4 1 78 20 32 79 2.4 1 72 7 33 94 2.4 1 78 16 34 111 2.4 1 96 15 35 103 2.4 1 89 14 36 98 2.4 1 86 12 37 98 2.4 1 88 10 38 87 2.4 1 85 2 39 109 2.4 1 94 15 40 110 2.4 1 96 14 41 110 2.4 1 97 13 42 134 2.4 1 106 28 43 116 2.4 1 104 12 44 125 2.4 1 111 14 45 124 2.4 1 110 14 46 122 2.4 1 110 12 47 140 2.4 1 127 13 48 152 2.4 1 136 16 49 127 2.4 1 110 17 50 138 2.4 1 123 15 51 152 2.4 1 137 15 52 142 2.4 1 131 11 53 154 2.4 1 137 17 54 114 2.4 1 106 8 55 133 2.4 1 123 10 56 123 2.4 1 107 16 57 167 2.4 1 154 13 58 161 2.4 1 135 26 59 142 2.4 1 125 17 60 123 2.4 1 111 12 61 121 2.4 1 104 17 62 163 2.4 1 144 19 63 135 2.4 1 125 10 64 166 2.4 1 153 13 65 148 2.4 1 134 14 66 162 2.4 1 150 12 67 187 2.4 1 164 23 68 177 2.4 1 155 22 69 176 2.4 1 173 3 70 141 2.4 1 131 10 71 176 2.4 1 155 21 72 159 2.4 1 139 20 73 167 2.4 1 146 21 74 177 2.4 1 158 19 75 183 2.4 1 162 21 76 202 2.4 1 179 23 77 214 2.4 1 199 15 78 195 2.4 1 174 21 79 183 2.4 1 168 15 80 179 2.4 1 161 18 81 195 2.4 1 167 28 82 215 2.4 1 199 16 83 192 2.4 1 169 23 84 183 2.4 1 158 25 85 188 2.4 1 161 27 86 177 2.4 1 151 26 87 184 2.4 1 164 20 88 201 2.4 1 179 22 89 189 2.4 1 172 17 90 217 2.4 1 192 25 91 210 2.4 1 190 20 92 227 2.4 1 210 17 93 210 2.4 1 190 20 94 154 2.4 1 135 19 95 200 2.4 1 172 28 96 166 2.4 1 139 27 97 205 2.4 1 177 28 98 222 2.4 1 204 18 99 202 2.4 1 174 28 100 185 2.4 1 166 19 101 202 2.4 1 178 24 102 208 2.4 1 176 32 103 220 2.4 1 193 27 104 196 2.4 1 156 40 105 197 2.4 1 171 26 106 197 2.4 1 176 21 107 220 2.4 1 188 32 108 239 2.4 1 221 18 109 238 2.4 1 208 30 110 243 2.4 1 220 23 111 222 2.4 1 194 28 112 228 2.4 1 205 23 113 231 2.4 1 205 26 114 234 2.4 1 199 35 115 245 2.4 1 213 32 116 220 2.4 1 195 25 117 235 2.4 1 213 22 118 239 2.4 1 212 27 119 262 2.4 1 229 33 120 294 2.4 1 265 29 121 278 2.4 1 241 37 122 242 2.4 1 218 24 123 238 2.4 1 208 30 124 219 2.4 1 183 36 125 234 2.4 1 204 30 126 261 2.4 1 228 33 127 296 2.4 1 241 55 128 342 2.4 1 303 39 129 289 2.4 1 263 26 130 300 2.4 1 251 49 131 343 2.4 1 294 49 132 308 2.4 1 273 35 133 351 2.4 1 285 66 134 357 2.4 1 265 92 135 496 2.4 1 213 283 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R2.fq.gz ============================================= 163170949 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 163170949 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1712731 (1.05%)