SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_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_2_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4774.64 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 168,555,919 Reads with adapters: 64,689,343 (38.4%) Reads written (passing filters): 168,555,919 (100.0%) Total basepairs processed: 20,137,031,441 bp Quality-trimmed: 4,088,114 bp (0.0%) Total written (filtered): 20,050,187,834 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64689343 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.1% C: 9.8% G: 7.4% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 54711066 42138979.8 0 54711066 2 6708849 10534744.9 0 6708849 3 1429411 2633686.2 0 1429411 4 1180167 658421.6 0 1180167 5 380029 164605.4 0 380029 6 93234 41151.3 0 93234 7 61148 10287.8 0 61148 8 36803 2572.0 0 36803 9 6988 643.0 0 5364 1624 10 60809 160.7 1 57364 3445 11 657 40.2 1 121 536 12 274 10.0 1 157 117 13 176 2.5 1 147 29 14 51 2.5 1 39 12 15 104 2.5 1 84 20 16 46 2.5 1 31 15 17 46 2.5 1 36 10 18 108 2.5 1 97 11 19 115 2.5 1 100 15 20 110 2.5 1 97 13 21 84 2.5 1 75 9 22 68 2.5 1 59 9 23 125 2.5 1 119 6 24 61 2.5 1 53 8 25 76 2.5 1 69 7 26 75 2.5 1 59 16 27 72 2.5 1 58 14 28 71 2.5 1 59 12 29 69 2.5 1 59 10 30 68 2.5 1 59 9 31 76 2.5 1 68 8 32 92 2.5 1 77 15 33 85 2.5 1 78 7 34 104 2.5 1 93 11 35 95 2.5 1 90 5 36 88 2.5 1 81 7 37 97 2.5 1 85 12 38 102 2.5 1 92 10 39 117 2.5 1 103 14 40 99 2.5 1 93 6 41 91 2.5 1 82 9 42 108 2.5 1 98 10 43 101 2.5 1 85 16 44 102 2.5 1 89 13 45 127 2.5 1 115 12 46 120 2.5 1 103 17 47 107 2.5 1 100 7 48 99 2.5 1 88 11 49 102 2.5 1 89 13 50 101 2.5 1 88 13 51 98 2.5 1 86 12 52 134 2.5 1 124 10 53 121 2.5 1 100 21 54 107 2.5 1 97 10 55 111 2.5 1 101 10 56 104 2.5 1 87 17 57 149 2.5 1 129 20 58 135 2.5 1 121 14 59 127 2.5 1 121 6 60 142 2.5 1 116 26 61 131 2.5 1 113 18 62 114 2.5 1 93 21 63 145 2.5 1 136 9 64 107 2.5 1 94 13 65 149 2.5 1 130 19 66 160 2.5 1 141 19 67 169 2.5 1 149 20 68 118 2.5 1 105 13 69 150 2.5 1 136 14 70 147 2.5 1 134 13 71 157 2.5 1 135 22 72 153 2.5 1 122 31 73 132 2.5 1 119 13 74 167 2.5 1 148 19 75 154 2.5 1 135 19 76 165 2.5 1 145 20 77 148 2.5 1 123 25 78 173 2.5 1 149 24 79 172 2.5 1 154 18 80 139 2.5 1 119 20 81 192 2.5 1 172 20 82 163 2.5 1 147 16 83 144 2.5 1 122 22 84 180 2.5 1 156 24 85 159 2.5 1 142 17 86 157 2.5 1 140 17 87 173 2.5 1 155 18 88 154 2.5 1 147 7 89 162 2.5 1 144 18 90 210 2.5 1 191 19 91 159 2.5 1 138 21 92 200 2.5 1 172 28 93 147 2.5 1 127 20 94 162 2.5 1 140 22 95 197 2.5 1 180 17 96 194 2.5 1 176 18 97 178 2.5 1 149 29 98 185 2.5 1 169 16 99 204 2.5 1 182 22 100 157 2.5 1 141 16 101 191 2.5 1 157 34 102 189 2.5 1 164 25 103 200 2.5 1 182 18 104 197 2.5 1 176 21 105 173 2.5 1 141 32 106 197 2.5 1 177 20 107 169 2.5 1 157 12 108 210 2.5 1 183 27 109 194 2.5 1 172 22 110 207 2.5 1 172 35 111 246 2.5 1 215 31 112 193 2.5 1 175 18 113 212 2.5 1 181 31 114 223 2.5 1 194 29 115 225 2.5 1 200 25 116 218 2.5 1 189 29 117 215 2.5 1 195 20 118 252 2.5 1 227 25 119 261 2.5 1 245 16 120 234 2.5 1 213 21 121 257 2.5 1 225 32 122 285 2.5 1 253 32 123 195 2.5 1 180 15 124 226 2.5 1 202 24 125 275 2.5 1 242 33 126 262 2.5 1 222 40 127 299 2.5 1 268 31 128 294 2.5 1 278 16 129 296 2.5 1 256 40 130 318 2.5 1 288 30 131 296 2.5 1 250 46 132 338 2.5 1 306 32 133 320 2.5 1 278 42 134 361 2.5 1 260 101 135 487 2.5 1 243 244 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R2.fq.gz ============================================= 168555919 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 168555919 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1587165 (0.94%)