SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_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_3_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5301.72 s (28 µs/read; 2.16 M reads/minute). === Summary === Total reads processed: 190,890,981 Reads with adapters: 67,946,267 (35.6%) Reads written (passing filters): 190,890,981 (100.0%) Total basepairs processed: 21,887,812,359 bp Quality-trimmed: 4,711,467 bp (0.0%) Total written (filtered): 21,792,339,028 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 67946267 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.0% C: 9.5% G: 8.2% T: 39.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 55407052 47722745.2 0 55407052 2 8405082 11930686.3 0 8405082 3 1609571 2982671.6 0 1609571 4 1478104 745667.9 0 1478104 5 578773 186417.0 0 578773 6 146091 46604.2 0 146091 7 102698 11651.1 0 102698 8 67699 2912.8 0 67699 9 12611 728.2 0 10073 2538 10 120983 182.0 1 116248 4735 11 969 45.5 1 189 780 12 240 11.4 1 83 157 13 70 2.8 1 42 28 14 49 2.8 1 39 10 15 105 2.8 1 89 16 16 37 2.8 1 24 13 17 32 2.8 1 20 12 18 89 2.8 1 77 12 19 87 2.8 1 70 17 20 126 2.8 1 111 15 21 58 2.8 1 50 8 22 41 2.8 1 31 10 23 115 2.8 1 107 8 24 83 2.8 1 74 9 25 74 2.8 1 67 7 26 61 2.8 1 48 13 27 62 2.8 1 56 6 28 67 2.8 1 59 8 29 66 2.8 1 56 10 30 53 2.8 1 43 10 31 54 2.8 1 41 13 32 76 2.8 1 66 10 33 68 2.8 1 64 4 34 61 2.8 1 52 9 35 61 2.8 1 53 8 36 79 2.8 1 68 11 37 75 2.8 1 65 10 38 94 2.8 1 74 20 39 82 2.8 1 67 15 40 78 2.8 1 64 14 41 74 2.8 1 69 5 42 87 2.8 1 75 12 43 80 2.8 1 74 6 44 90 2.8 1 83 7 45 93 2.8 1 83 10 46 85 2.8 1 75 10 47 73 2.8 1 66 7 48 80 2.8 1 72 8 49 104 2.8 1 97 7 50 103 2.8 1 86 17 51 102 2.8 1 89 13 52 92 2.8 1 76 16 53 91 2.8 1 77 14 54 86 2.8 1 76 10 55 99 2.8 1 90 9 56 115 2.8 1 98 17 57 101 2.8 1 88 13 58 113 2.8 1 91 22 59 125 2.8 1 114 11 60 114 2.8 1 107 7 61 108 2.8 1 104 4 62 115 2.8 1 97 18 63 92 2.8 1 83 9 64 88 2.8 1 80 8 65 112 2.8 1 104 8 66 125 2.8 1 114 11 67 132 2.8 1 117 15 68 111 2.8 1 100 11 69 133 2.8 1 115 18 70 135 2.8 1 127 8 71 141 2.8 1 123 18 72 110 2.8 1 92 18 73 129 2.8 1 121 8 74 117 2.8 1 105 12 75 149 2.8 1 133 16 76 149 2.8 1 128 21 77 138 2.8 1 112 26 78 114 2.8 1 94 20 79 138 2.8 1 120 18 80 143 2.8 1 126 17 81 125 2.8 1 111 14 82 133 2.8 1 122 11 83 162 2.8 1 154 8 84 142 2.8 1 126 16 85 158 2.8 1 131 27 86 147 2.8 1 131 16 87 153 2.8 1 140 13 88 148 2.8 1 136 12 89 164 2.8 1 141 23 90 165 2.8 1 138 27 91 145 2.8 1 130 15 92 157 2.8 1 138 19 93 181 2.8 1 154 27 94 141 2.8 1 120 21 95 138 2.8 1 121 17 96 161 2.8 1 143 18 97 154 2.8 1 120 34 98 152 2.8 1 120 32 99 167 2.8 1 149 18 100 177 2.8 1 162 15 101 179 2.8 1 157 22 102 169 2.8 1 143 26 103 161 2.8 1 123 38 104 146 2.8 1 132 14 105 154 2.8 1 135 19 106 180 2.8 1 162 18 107 153 2.8 1 132 21 108 157 2.8 1 132 25 109 162 2.8 1 149 13 110 179 2.8 1 161 18 111 216 2.8 1 193 23 112 154 2.8 1 131 23 113 165 2.8 1 148 17 114 185 2.8 1 163 22 115 172 2.8 1 150 22 116 175 2.8 1 151 24 117 198 2.8 1 177 21 118 168 2.8 1 140 28 119 219 2.8 1 187 32 120 198 2.8 1 168 30 121 170 2.8 1 148 22 122 227 2.8 1 204 23 123 182 2.8 1 160 22 124 194 2.8 1 151 43 125 193 2.8 1 172 21 126 201 2.8 1 183 18 127 211 2.8 1 186 25 128 231 2.8 1 199 32 129 248 2.8 1 214 34 130 230 2.8 1 205 25 131 255 2.8 1 223 32 132 239 2.8 1 195 44 133 247 2.8 1 209 38 134 248 2.8 1 187 61 135 369 2.8 1 169 200 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R1.fq.gz ============================================= 190890981 sequences processed in total