SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_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_8_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4519.25 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 163,170,949 Reads with adapters: 60,377,927 (37.0%) Reads written (passing filters): 163,170,949 (100.0%) Total basepairs processed: 19,050,779,988 bp Quality-trimmed: 4,388,508 bp (0.0%) Total written (filtered): 18,967,646,504 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60377927 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.4% C: 9.7% G: 7.9% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 50084126 40792737.2 0 50084126 2 7045447 10198184.3 0 7045447 3 1408521 2549546.1 0 1408521 4 1194884 637386.5 0 1194884 5 371081 159346.6 0 371081 6 91420 39836.7 0 91420 7 61796 9959.2 0 61796 8 38927 2489.8 0 38927 9 6561 622.4 0 4812 1749 10 53488 155.6 1 50006 3482 11 580 38.9 1 108 472 12 222 9.7 1 114 108 13 71 2.4 1 57 14 14 55 2.4 1 45 10 15 133 2.4 1 119 14 16 44 2.4 1 33 11 17 60 2.4 1 52 8 18 117 2.4 1 104 13 19 114 2.4 1 95 19 20 148 2.4 1 132 16 21 85 2.4 1 75 10 22 67 2.4 1 60 7 23 152 2.4 1 128 24 24 96 2.4 1 88 8 25 107 2.4 1 94 13 26 104 2.4 1 87 17 27 99 2.4 1 87 12 28 91 2.4 1 86 5 29 66 2.4 1 56 10 30 80 2.4 1 74 6 31 83 2.4 1 74 9 32 85 2.4 1 78 7 33 90 2.4 1 79 11 34 101 2.4 1 91 10 35 117 2.4 1 102 15 36 83 2.4 1 72 11 37 112 2.4 1 98 14 38 109 2.4 1 94 15 39 98 2.4 1 90 8 40 107 2.4 1 98 9 41 100 2.4 1 91 9 42 120 2.4 1 110 10 43 88 2.4 1 77 11 44 116 2.4 1 98 18 45 116 2.4 1 106 10 46 121 2.4 1 113 8 47 96 2.4 1 80 16 48 133 2.4 1 126 7 49 106 2.4 1 98 8 50 117 2.4 1 110 7 51 139 2.4 1 131 8 52 142 2.4 1 124 18 53 131 2.4 1 116 15 54 135 2.4 1 115 20 55 143 2.4 1 127 16 56 145 2.4 1 124 21 57 150 2.4 1 136 14 58 137 2.4 1 124 13 59 117 2.4 1 107 10 60 126 2.4 1 118 8 61 130 2.4 1 119 11 62 147 2.4 1 137 10 63 154 2.4 1 137 17 64 117 2.4 1 102 15 65 159 2.4 1 144 15 66 174 2.4 1 150 24 67 145 2.4 1 122 23 68 159 2.4 1 143 16 69 169 2.4 1 156 13 70 156 2.4 1 143 13 71 151 2.4 1 136 15 72 187 2.4 1 172 15 73 180 2.4 1 162 18 74 156 2.4 1 145 11 75 150 2.4 1 139 11 76 174 2.4 1 147 27 77 206 2.4 1 184 22 78 174 2.4 1 157 17 79 147 2.4 1 130 17 80 166 2.4 1 154 12 81 200 2.4 1 187 13 82 165 2.4 1 148 17 83 178 2.4 1 156 22 84 159 2.4 1 143 16 85 191 2.4 1 168 23 86 204 2.4 1 179 25 87 189 2.4 1 170 19 88 207 2.4 1 182 25 89 193 2.4 1 175 18 90 189 2.4 1 169 20 91 187 2.4 1 180 7 92 178 2.4 1 157 21 93 186 2.4 1 169 17 94 189 2.4 1 165 24 95 211 2.4 1 195 16 96 185 2.4 1 161 24 97 213 2.4 1 188 25 98 208 2.4 1 190 18 99 199 2.4 1 180 19 100 227 2.4 1 203 24 101 224 2.4 1 199 25 102 219 2.4 1 197 22 103 214 2.4 1 191 23 104 192 2.4 1 171 21 105 216 2.4 1 187 29 106 224 2.4 1 193 31 107 199 2.4 1 182 17 108 170 2.4 1 148 22 109 199 2.4 1 162 37 110 192 2.4 1 164 28 111 224 2.4 1 198 26 112 214 2.4 1 178 36 113 190 2.4 1 165 25 114 233 2.4 1 194 39 115 188 2.4 1 163 25 116 209 2.4 1 181 28 117 233 2.4 1 212 21 118 242 2.4 1 214 28 119 242 2.4 1 202 40 120 238 2.4 1 201 37 121 235 2.4 1 204 31 122 220 2.4 1 189 31 123 248 2.4 1 222 26 124 244 2.4 1 217 27 125 250 2.4 1 220 30 126 251 2.4 1 226 25 127 273 2.4 1 243 30 128 277 2.4 1 243 34 129 290 2.4 1 264 26 130 309 2.4 1 274 35 131 308 2.4 1 262 46 132 312 2.4 1 283 29 133 317 2.4 1 256 61 134 361 2.4 1 258 103 135 506 2.4 1 222 284 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R1.fq.gz ============================================= 163170949 sequences processed in total