SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_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_5_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4093.54 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 150,419,008 Reads with adapters: 54,717,652 (36.4%) Reads written (passing filters): 150,419,008 (100.0%) Total basepairs processed: 17,426,503,375 bp Quality-trimmed: 4,558,367 bp (0.0%) Total written (filtered): 17,349,807,948 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54717652 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.6% G: 8.0% T: 39.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 45101075 37604752.0 0 45101075 2 6503750 9401188.0 0 6503750 3 1259619 2350297.0 0 1259619 4 1135277 587574.2 0 1135277 5 401524 146893.6 0 401524 6 100353 36723.4 0 100353 7 71462 9180.8 0 71462 8 46543 2295.2 0 46543 9 8283 573.8 0 6448 1835 10 72512 143.5 1 69038 3474 11 690 35.9 1 158 532 12 243 9.0 1 116 127 13 173 2.2 1 150 23 14 36 2.2 1 27 9 15 95 2.2 1 84 11 16 21 2.2 1 20 1 17 37 2.2 1 30 7 18 78 2.2 1 73 5 19 72 2.2 1 59 13 20 106 2.2 1 98 8 21 50 2.2 1 46 4 22 51 2.2 1 41 10 23 101 2.2 1 95 6 24 54 2.2 1 43 11 25 70 2.2 1 57 13 26 63 2.2 1 54 9 27 83 2.2 1 76 7 28 66 2.2 1 60 6 29 52 2.2 1 41 11 30 64 2.2 1 49 15 31 68 2.2 1 63 5 32 52 2.2 1 43 9 33 72 2.2 1 55 17 34 61 2.2 1 51 10 35 81 2.2 1 64 17 36 62 2.2 1 53 9 37 66 2.2 1 61 5 38 73 2.2 1 61 12 39 94 2.2 1 75 19 40 89 2.2 1 76 13 41 87 2.2 1 75 12 42 85 2.2 1 72 13 43 82 2.2 1 74 8 44 85 2.2 1 71 14 45 84 2.2 1 74 10 46 95 2.2 1 82 13 47 96 2.2 1 80 16 48 103 2.2 1 88 15 49 114 2.2 1 107 7 50 109 2.2 1 94 15 51 95 2.2 1 82 13 52 127 2.2 1 111 16 53 78 2.2 1 64 14 54 101 2.2 1 88 13 55 124 2.2 1 106 18 56 129 2.2 1 117 12 57 120 2.2 1 104 16 58 111 2.2 1 98 13 59 106 2.2 1 91 15 60 111 2.2 1 100 11 61 114 2.2 1 93 21 62 123 2.2 1 113 10 63 110 2.2 1 102 8 64 122 2.2 1 115 7 65 121 2.2 1 104 17 66 123 2.2 1 113 10 67 111 2.2 1 97 14 68 139 2.2 1 115 24 69 133 2.2 1 121 12 70 129 2.2 1 117 12 71 128 2.2 1 120 8 72 119 2.2 1 105 14 73 116 2.2 1 108 8 74 141 2.2 1 129 12 75 140 2.2 1 126 14 76 156 2.2 1 148 8 77 163 2.2 1 147 16 78 142 2.2 1 123 19 79 131 2.2 1 116 15 80 141 2.2 1 121 20 81 125 2.2 1 105 20 82 144 2.2 1 125 19 83 142 2.2 1 126 16 84 143 2.2 1 122 21 85 169 2.2 1 142 27 86 143 2.2 1 133 10 87 136 2.2 1 116 20 88 122 2.2 1 105 17 89 162 2.2 1 148 14 90 164 2.2 1 153 11 91 147 2.2 1 119 28 92 147 2.2 1 130 17 93 132 2.2 1 105 27 94 151 2.2 1 131 20 95 186 2.2 1 169 17 96 156 2.2 1 125 31 97 140 2.2 1 128 12 98 140 2.2 1 129 11 99 183 2.2 1 163 20 100 191 2.2 1 164 27 101 133 2.2 1 117 16 102 183 2.2 1 161 22 103 120 2.2 1 108 12 104 156 2.2 1 128 28 105 126 2.2 1 107 19 106 158 2.2 1 139 19 107 161 2.2 1 140 21 108 150 2.2 1 138 12 109 172 2.2 1 151 21 110 134 2.2 1 125 9 111 172 2.2 1 150 22 112 196 2.2 1 176 20 113 172 2.2 1 149 23 114 194 2.2 1 167 27 115 139 2.2 1 120 19 116 148 2.2 1 133 15 117 169 2.2 1 152 17 118 178 2.2 1 150 28 119 162 2.2 1 149 13 120 191 2.2 1 168 23 121 223 2.2 1 194 29 122 202 2.2 1 178 24 123 193 2.2 1 167 26 124 181 2.2 1 142 39 125 192 2.2 1 169 23 126 222 2.2 1 192 30 127 204 2.2 1 178 26 128 204 2.2 1 181 23 129 202 2.2 1 179 23 130 236 2.2 1 200 36 131 261 2.2 1 233 28 132 266 2.2 1 244 22 133 270 2.2 1 227 43 134 233 2.2 1 160 73 135 361 2.2 1 141 220 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R2.fq.gz ============================================= 150419008 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 150419008 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1715117 (1.14%)