SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_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_5_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4110.42 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 150,419,008 Reads with adapters: 55,059,110 (36.6%) Reads written (passing filters): 150,419,008 (100.0%) Total basepairs processed: 17,427,703,814 bp Quality-trimmed: 4,672,609 bp (0.0%) Total written (filtered): 17,350,375,657 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55059110 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.1% C: 9.7% G: 8.1% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 45286525 37604752.0 0 45286525 2 6611329 9401188.0 0 6611329 3 1310029 2350297.0 0 1310029 4 1131557 587574.2 0 1131557 5 401467 146893.6 0 401467 6 101925 36723.4 0 101925 7 71237 9180.8 0 71237 8 46703 2295.2 0 46703 9 8117 573.8 0 6313 1804 10 73478 143.5 1 69860 3618 11 673 35.9 1 134 539 12 201 9.0 1 96 105 13 65 2.2 1 40 25 14 46 2.2 1 37 9 15 79 2.2 1 67 12 16 34 2.2 1 28 6 17 27 2.2 1 21 6 18 90 2.2 1 74 16 19 98 2.2 1 81 17 20 106 2.2 1 88 18 21 78 2.2 1 67 11 22 47 2.2 1 39 8 23 111 2.2 1 100 11 24 62 2.2 1 60 2 25 86 2.2 1 75 11 26 59 2.2 1 54 5 27 85 2.2 1 74 11 28 57 2.2 1 48 9 29 59 2.2 1 52 7 30 77 2.2 1 65 12 31 67 2.2 1 56 11 32 56 2.2 1 50 6 33 92 2.2 1 83 9 34 64 2.2 1 53 11 35 68 2.2 1 57 11 36 52 2.2 1 47 5 37 68 2.2 1 58 10 38 66 2.2 1 59 7 39 82 2.2 1 76 6 40 74 2.2 1 63 11 41 114 2.2 1 103 11 42 85 2.2 1 82 3 43 86 2.2 1 70 16 44 90 2.2 1 81 9 45 80 2.2 1 70 10 46 77 2.2 1 66 11 47 81 2.2 1 65 16 48 95 2.2 1 84 11 49 93 2.2 1 76 17 50 105 2.2 1 77 28 51 86 2.2 1 83 3 52 92 2.2 1 80 12 53 84 2.2 1 73 11 54 80 2.2 1 74 6 55 122 2.2 1 112 10 56 101 2.2 1 95 6 57 109 2.2 1 91 18 58 104 2.2 1 96 8 59 140 2.2 1 130 10 60 109 2.2 1 87 22 61 115 2.2 1 102 13 62 115 2.2 1 98 17 63 136 2.2 1 117 19 64 136 2.2 1 119 17 65 107 2.2 1 95 12 66 119 2.2 1 106 13 67 128 2.2 1 114 14 68 115 2.2 1 98 17 69 115 2.2 1 106 9 70 119 2.2 1 106 13 71 110 2.2 1 98 12 72 142 2.2 1 128 14 73 123 2.2 1 114 9 74 123 2.2 1 110 13 75 103 2.2 1 84 19 76 139 2.2 1 126 13 77 184 2.2 1 170 14 78 145 2.2 1 130 15 79 128 2.2 1 116 12 80 142 2.2 1 130 12 81 115 2.2 1 104 11 82 137 2.2 1 126 11 83 143 2.2 1 128 15 84 119 2.2 1 111 8 85 138 2.2 1 125 13 86 132 2.2 1 119 13 87 140 2.2 1 126 14 88 135 2.2 1 123 12 89 155 2.2 1 141 14 90 143 2.2 1 127 16 91 135 2.2 1 120 15 92 124 2.2 1 112 12 93 152 2.2 1 133 19 94 129 2.2 1 114 15 95 112 2.2 1 93 19 96 146 2.2 1 131 15 97 146 2.2 1 124 22 98 146 2.2 1 126 20 99 182 2.2 1 163 19 100 165 2.2 1 147 18 101 142 2.2 1 127 15 102 154 2.2 1 133 21 103 150 2.2 1 136 14 104 176 2.2 1 155 21 105 155 2.2 1 132 23 106 153 2.2 1 141 12 107 142 2.2 1 122 20 108 149 2.2 1 132 17 109 162 2.2 1 146 16 110 155 2.2 1 136 19 111 162 2.2 1 132 30 112 167 2.2 1 156 11 113 189 2.2 1 173 16 114 162 2.2 1 152 10 115 134 2.2 1 121 13 116 157 2.2 1 138 19 117 198 2.2 1 170 28 118 187 2.2 1 168 19 119 213 2.2 1 190 23 120 196 2.2 1 178 18 121 183 2.2 1 157 26 122 203 2.2 1 179 24 123 140 2.2 1 117 23 124 186 2.2 1 157 29 125 185 2.2 1 149 36 126 192 2.2 1 169 23 127 229 2.2 1 212 17 128 233 2.2 1 205 28 129 235 2.2 1 211 24 130 246 2.2 1 223 23 131 222 2.2 1 189 33 132 234 2.2 1 215 19 133 240 2.2 1 195 45 134 246 2.2 1 167 79 135 366 2.2 1 152 214 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R1.fq.gz ============================================= 150419008 sequences processed in total