SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_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_1_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4611.37 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 162,780,101 Reads with adapters: 62,280,853 (38.3%) Reads written (passing filters): 162,780,101 (100.0%) Total basepairs processed: 19,461,874,095 bp Quality-trimmed: 3,835,880 bp (0.0%) Total written (filtered): 19,378,440,979 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62280853 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.1% C: 9.8% G: 7.6% T: 38.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 52600766 40695025.2 0 52600766 2 6526277 10173756.3 0 6526277 3 1379477 2543439.1 0 1379477 4 1137096 635859.8 0 1137096 5 366365 158964.9 0 366365 6 89932 39741.2 0 89932 7 59322 9935.3 0 59322 8 35528 2483.8 0 35528 9 6643 621.0 0 5024 1619 10 61870 155.2 1 58490 3380 11 580 38.8 1 125 455 12 220 9.7 1 123 97 13 155 2.4 1 135 20 14 41 2.4 1 30 11 15 81 2.4 1 76 5 16 37 2.4 1 32 5 17 43 2.4 1 31 12 18 87 2.4 1 80 7 19 72 2.4 1 65 7 20 102 2.4 1 84 18 21 66 2.4 1 49 17 22 39 2.4 1 32 7 23 86 2.4 1 78 8 24 71 2.4 1 64 7 25 71 2.4 1 64 7 26 72 2.4 1 63 9 27 68 2.4 1 62 6 28 55 2.4 1 46 9 29 67 2.4 1 54 13 30 48 2.4 1 42 6 31 56 2.4 1 48 8 32 86 2.4 1 73 13 33 56 2.4 1 53 3 34 57 2.4 1 44 13 35 63 2.4 1 57 6 36 66 2.4 1 58 8 37 68 2.4 1 56 12 38 62 2.4 1 56 6 39 54 2.4 1 43 11 40 73 2.4 1 65 8 41 83 2.4 1 75 8 42 64 2.4 1 56 8 43 58 2.4 1 53 5 44 81 2.4 1 73 8 45 80 2.4 1 72 8 46 93 2.4 1 81 12 47 106 2.4 1 94 12 48 99 2.4 1 89 10 49 72 2.4 1 62 10 50 103 2.4 1 93 10 51 113 2.4 1 97 16 52 80 2.4 1 69 11 53 109 2.4 1 100 9 54 106 2.4 1 100 6 55 110 2.4 1 95 15 56 108 2.4 1 96 12 57 114 2.4 1 105 9 58 110 2.4 1 99 11 59 89 2.4 1 79 10 60 109 2.4 1 100 9 61 125 2.4 1 108 17 62 118 2.4 1 102 16 63 91 2.4 1 80 11 64 117 2.4 1 110 7 65 117 2.4 1 107 10 66 95 2.4 1 85 10 67 129 2.4 1 118 11 68 123 2.4 1 112 11 69 114 2.4 1 102 12 70 131 2.4 1 124 7 71 137 2.4 1 125 12 72 89 2.4 1 79 10 73 150 2.4 1 126 24 74 147 2.4 1 126 21 75 118 2.4 1 101 17 76 110 2.4 1 96 14 77 141 2.4 1 120 21 78 141 2.4 1 129 12 79 143 2.4 1 130 13 80 144 2.4 1 134 10 81 157 2.4 1 135 22 82 140 2.4 1 127 13 83 151 2.4 1 128 23 84 137 2.4 1 118 19 85 120 2.4 1 105 15 86 131 2.4 1 115 16 87 133 2.4 1 120 13 88 160 2.4 1 140 20 89 139 2.4 1 127 12 90 172 2.4 1 153 19 91 158 2.4 1 138 20 92 138 2.4 1 123 15 93 142 2.4 1 130 12 94 150 2.4 1 132 18 95 162 2.4 1 142 20 96 149 2.4 1 129 20 97 188 2.4 1 163 25 98 135 2.4 1 119 16 99 163 2.4 1 149 14 100 170 2.4 1 147 23 101 169 2.4 1 151 18 102 148 2.4 1 121 27 103 141 2.4 1 119 22 104 143 2.4 1 124 19 105 131 2.4 1 118 13 106 163 2.4 1 140 23 107 173 2.4 1 148 25 108 154 2.4 1 128 26 109 163 2.4 1 137 26 110 216 2.4 1 200 16 111 185 2.4 1 161 24 112 212 2.4 1 185 27 113 169 2.4 1 151 18 114 194 2.4 1 171 23 115 184 2.4 1 173 11 116 184 2.4 1 165 19 117 208 2.4 1 183 25 118 216 2.4 1 193 23 119 182 2.4 1 154 28 120 249 2.4 1 232 17 121 222 2.4 1 205 17 122 187 2.4 1 172 15 123 194 2.4 1 176 18 124 193 2.4 1 167 26 125 232 2.4 1 198 34 126 204 2.4 1 191 13 127 252 2.4 1 225 27 128 261 2.4 1 232 29 129 273 2.4 1 239 34 130 279 2.4 1 247 32 131 286 2.4 1 262 24 132 296 2.4 1 249 47 133 293 2.4 1 248 45 134 321 2.4 1 243 78 135 436 2.4 1 198 238 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.fq.gz ============================================= 162780101 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 162780101 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1543746 (0.95%)