SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_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_2_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4803.25 s (28 µs/read; 2.11 M reads/minute). === Summary === Total reads processed: 168,555,919 Reads with adapters: 64,789,951 (38.4%) Reads written (passing filters): 168,555,919 (100.0%) Total basepairs processed: 20,136,253,714 bp Quality-trimmed: 4,613,448 bp (0.0%) Total written (filtered): 20,048,443,536 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64789951 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.8% C: 10.0% G: 7.6% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 54553749 42138979.8 0 54553749 2 6934950 10534744.9 0 6934950 3 1459472 2633686.2 0 1459472 4 1175875 658421.6 0 1175875 5 382331 164605.4 0 382331 6 95249 41151.3 0 95249 7 61926 10287.8 0 61926 8 36466 2572.0 0 36466 9 6653 643.0 0 4823 1830 10 62077 160.7 1 58567 3510 11 661 40.2 1 144 517 12 233 10.0 1 136 97 13 80 2.5 1 56 24 14 69 2.5 1 52 17 15 100 2.5 1 84 16 16 53 2.5 1 38 15 17 50 2.5 1 41 9 18 113 2.5 1 94 19 19 140 2.5 1 115 25 20 138 2.5 1 124 14 21 68 2.5 1 56 12 22 75 2.5 1 56 19 23 126 2.5 1 117 9 24 81 2.5 1 64 17 25 100 2.5 1 87 13 26 81 2.5 1 74 7 27 97 2.5 1 85 12 28 79 2.5 1 63 16 29 76 2.5 1 65 11 30 61 2.5 1 51 10 31 86 2.5 1 65 21 32 103 2.5 1 96 7 33 100 2.5 1 86 14 34 92 2.5 1 82 10 35 106 2.5 1 94 12 36 83 2.5 1 69 14 37 91 2.5 1 79 12 38 74 2.5 1 64 10 39 106 2.5 1 91 15 40 99 2.5 1 86 13 41 96 2.5 1 84 12 42 90 2.5 1 80 10 43 97 2.5 1 87 10 44 101 2.5 1 89 12 45 115 2.5 1 104 11 46 103 2.5 1 87 16 47 111 2.5 1 95 16 48 121 2.5 1 108 13 49 99 2.5 1 89 10 50 123 2.5 1 105 18 51 110 2.5 1 99 11 52 102 2.5 1 93 9 53 117 2.5 1 97 20 54 118 2.5 1 105 13 55 102 2.5 1 88 14 56 121 2.5 1 106 15 57 116 2.5 1 94 22 58 137 2.5 1 119 18 59 158 2.5 1 144 14 60 141 2.5 1 128 13 61 124 2.5 1 111 13 62 148 2.5 1 120 28 63 121 2.5 1 108 13 64 145 2.5 1 130 15 65 166 2.5 1 155 11 66 130 2.5 1 120 10 67 126 2.5 1 113 13 68 178 2.5 1 157 21 69 156 2.5 1 145 11 70 136 2.5 1 119 17 71 162 2.5 1 146 16 72 142 2.5 1 127 15 73 139 2.5 1 125 14 74 141 2.5 1 124 17 75 148 2.5 1 129 19 76 183 2.5 1 157 26 77 153 2.5 1 138 15 78 184 2.5 1 167 17 79 161 2.5 1 138 23 80 182 2.5 1 168 14 81 183 2.5 1 164 19 82 162 2.5 1 144 18 83 162 2.5 1 138 24 84 177 2.5 1 158 19 85 196 2.5 1 181 15 86 156 2.5 1 128 28 87 170 2.5 1 150 20 88 218 2.5 1 201 17 89 179 2.5 1 160 19 90 186 2.5 1 173 13 91 168 2.5 1 155 13 92 211 2.5 1 203 8 93 173 2.5 1 158 15 94 170 2.5 1 150 20 95 184 2.5 1 164 20 96 212 2.5 1 188 24 97 204 2.5 1 183 21 98 187 2.5 1 165 22 99 211 2.5 1 174 37 100 192 2.5 1 169 23 101 179 2.5 1 158 21 102 154 2.5 1 143 11 103 154 2.5 1 147 7 104 174 2.5 1 147 27 105 212 2.5 1 182 30 106 172 2.5 1 151 21 107 211 2.5 1 186 25 108 199 2.5 1 179 20 109 211 2.5 1 192 19 110 213 2.5 1 189 24 111 218 2.5 1 202 16 112 209 2.5 1 185 24 113 239 2.5 1 214 25 114 172 2.5 1 166 6 115 225 2.5 1 196 29 116 219 2.5 1 197 22 117 249 2.5 1 218 31 118 246 2.5 1 222 24 119 282 2.5 1 252 30 120 218 2.5 1 198 20 121 232 2.5 1 206 26 122 234 2.5 1 204 30 123 240 2.5 1 214 26 124 252 2.5 1 214 38 125 254 2.5 1 211 43 126 274 2.5 1 246 28 127 294 2.5 1 263 31 128 303 2.5 1 264 39 129 294 2.5 1 266 28 130 343 2.5 1 295 48 131 373 2.5 1 332 41 132 327 2.5 1 295 32 133 329 2.5 1 287 42 134 370 2.5 1 278 92 135 503 2.5 1 239 264 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R1.fq.gz ============================================= 168555919 sequences processed in total