SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_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_4_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5752.90 s (29 µs/read; 2.09 M reads/minute). === Summary === Total reads processed: 199,920,896 Reads with adapters: 74,522,650 (37.3%) Reads written (passing filters): 199,920,896 (100.0%) Total basepairs processed: 23,464,661,406 bp Quality-trimmed: 5,134,686 bp (0.0%) Total written (filtered): 23,362,142,591 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74522650 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.6% C: 9.7% G: 7.8% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 62047657 49980224.0 0 62047657 2 8370995 12495056.0 0 8370995 3 1677009 3123764.0 0 1677009 4 1491904 780941.0 0 1491904 5 514799 195235.2 0 514799 6 131657 48808.8 0 131657 7 90622 12202.2 0 90622 8 60206 3050.6 0 60206 9 11770 762.6 0 9369 2401 10 102131 190.7 1 97298 4833 11 888 47.7 1 204 684 12 318 11.9 1 156 162 13 196 3.0 1 161 35 14 41 3.0 1 34 7 15 117 3.0 1 98 19 16 53 3.0 1 38 15 17 44 3.0 1 32 12 18 108 3.0 1 99 9 19 90 3.0 1 79 11 20 174 3.0 1 156 18 21 91 3.0 1 83 8 22 63 3.0 1 56 7 23 148 3.0 1 133 15 24 96 3.0 1 86 10 25 109 3.0 1 95 14 26 88 3.0 1 79 9 27 86 3.0 1 74 12 28 64 3.0 1 56 8 29 116 3.0 1 107 9 30 81 3.0 1 68 13 31 84 3.0 1 78 6 32 100 3.0 1 86 14 33 88 3.0 1 67 21 34 100 3.0 1 84 16 35 93 3.0 1 82 11 36 92 3.0 1 80 12 37 116 3.0 1 102 14 38 88 3.0 1 71 17 39 120 3.0 1 99 21 40 102 3.0 1 88 14 41 128 3.0 1 109 19 42 110 3.0 1 94 16 43 93 3.0 1 82 11 44 122 3.0 1 110 12 45 120 3.0 1 116 4 46 114 3.0 1 98 16 47 118 3.0 1 110 8 48 119 3.0 1 109 10 49 143 3.0 1 121 22 50 157 3.0 1 133 24 51 148 3.0 1 130 18 52 129 3.0 1 116 13 53 127 3.0 1 111 16 54 152 3.0 1 137 15 55 146 3.0 1 128 18 56 143 3.0 1 132 11 57 196 3.0 1 175 21 58 143 3.0 1 132 11 59 166 3.0 1 153 13 60 164 3.0 1 148 16 61 145 3.0 1 132 13 62 151 3.0 1 132 19 63 164 3.0 1 150 14 64 167 3.0 1 158 9 65 184 3.0 1 159 25 66 173 3.0 1 152 21 67 187 3.0 1 175 12 68 174 3.0 1 150 24 69 142 3.0 1 124 18 70 205 3.0 1 178 27 71 167 3.0 1 145 22 72 168 3.0 1 157 11 73 186 3.0 1 170 16 74 173 3.0 1 160 13 75 175 3.0 1 157 18 76 162 3.0 1 144 18 77 199 3.0 1 179 20 78 174 3.0 1 155 19 79 211 3.0 1 181 30 80 239 3.0 1 220 19 81 248 3.0 1 222 26 82 227 3.0 1 201 26 83 211 3.0 1 185 26 84 171 3.0 1 152 19 85 178 3.0 1 162 16 86 192 3.0 1 173 19 87 211 3.0 1 180 31 88 215 3.0 1 194 21 89 211 3.0 1 185 26 90 223 3.0 1 195 28 91 224 3.0 1 204 20 92 234 3.0 1 211 23 93 203 3.0 1 187 16 94 236 3.0 1 212 24 95 229 3.0 1 199 30 96 211 3.0 1 193 18 97 207 3.0 1 174 33 98 242 3.0 1 216 26 99 231 3.0 1 200 31 100 237 3.0 1 209 28 101 216 3.0 1 185 31 102 235 3.0 1 198 37 103 215 3.0 1 193 22 104 184 3.0 1 168 16 105 242 3.0 1 214 28 106 237 3.0 1 209 28 107 203 3.0 1 181 22 108 231 3.0 1 212 19 109 247 3.0 1 206 41 110 275 3.0 1 240 35 111 221 3.0 1 190 31 112 233 3.0 1 204 29 113 205 3.0 1 186 19 114 239 3.0 1 219 20 115 233 3.0 1 213 20 116 204 3.0 1 180 24 117 224 3.0 1 199 25 118 285 3.0 1 257 28 119 240 3.0 1 217 23 120 256 3.0 1 225 31 121 293 3.0 1 263 30 122 256 3.0 1 221 35 123 277 3.0 1 256 21 124 260 3.0 1 235 25 125 250 3.0 1 214 36 126 226 3.0 1 200 26 127 280 3.0 1 241 39 128 276 3.0 1 239 37 129 305 3.0 1 268 37 130 342 3.0 1 302 40 131 314 3.0 1 269 45 132 307 3.0 1 258 49 133 338 3.0 1 289 49 134 423 3.0 1 317 106 135 549 3.0 1 236 313 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R2.fq.gz ============================================= 199920896 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 199920896 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1926681 (0.96%)