SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_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_3_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5277.20 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 190,890,981 Reads with adapters: 68,104,946 (35.7%) Reads written (passing filters): 190,890,981 (100.0%) Total basepairs processed: 21,887,510,700 bp Quality-trimmed: 6,137,470 bp (0.0%) Total written (filtered): 21,790,702,726 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 68104946 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.2% C: 9.5% G: 8.0% T: 39.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 55768543 47722745.2 0 55768543 2 8249585 11930686.3 0 8249585 3 1573556 2982671.6 0 1573556 4 1483247 745667.9 0 1483247 5 567788 186417.0 0 567788 6 143673 46604.2 0 143673 7 102236 11651.1 0 102236 8 67227 2912.8 0 67227 9 12764 728.2 0 10115 2649 10 117979 182.0 1 113181 4798 11 962 45.5 1 195 767 12 345 11.4 1 205 140 13 190 2.8 1 145 45 14 43 2.8 1 29 14 15 88 2.8 1 71 17 16 29 2.8 1 24 5 17 36 2.8 1 28 8 18 79 2.8 1 65 14 19 68 2.8 1 60 8 20 130 2.8 1 117 13 21 68 2.8 1 58 10 22 48 2.8 1 37 11 23 105 2.8 1 96 9 24 44 2.8 1 40 4 25 73 2.8 1 65 8 26 67 2.8 1 57 10 27 62 2.8 1 51 11 28 71 2.8 1 57 14 29 48 2.8 1 40 8 30 72 2.8 1 64 8 31 65 2.8 1 57 8 32 73 2.8 1 62 11 33 70 2.8 1 60 10 34 90 2.8 1 80 10 35 80 2.8 1 74 6 36 75 2.8 1 65 10 37 87 2.8 1 79 8 38 70 2.8 1 60 10 39 94 2.8 1 81 13 40 77 2.8 1 68 9 41 88 2.8 1 77 11 42 77 2.8 1 69 8 43 103 2.8 1 83 20 44 96 2.8 1 87 9 45 88 2.8 1 81 7 46 91 2.8 1 76 15 47 84 2.8 1 73 11 48 102 2.8 1 92 10 49 97 2.8 1 83 14 50 91 2.8 1 83 8 51 85 2.8 1 74 11 52 116 2.8 1 104 12 53 93 2.8 1 79 14 54 88 2.8 1 79 9 55 120 2.8 1 115 5 56 128 2.8 1 117 11 57 116 2.8 1 108 8 58 112 2.8 1 105 7 59 109 2.8 1 99 10 60 122 2.8 1 103 19 61 112 2.8 1 103 9 62 103 2.8 1 90 13 63 122 2.8 1 106 16 64 108 2.8 1 96 12 65 124 2.8 1 105 19 66 121 2.8 1 107 14 67 114 2.8 1 106 8 68 137 2.8 1 122 15 69 137 2.8 1 118 19 70 137 2.8 1 118 19 71 124 2.8 1 109 15 72 133 2.8 1 118 15 73 139 2.8 1 124 15 74 155 2.8 1 135 20 75 122 2.8 1 109 13 76 141 2.8 1 130 11 77 161 2.8 1 139 22 78 132 2.8 1 118 14 79 142 2.8 1 125 17 80 143 2.8 1 127 16 81 144 2.8 1 126 18 82 144 2.8 1 120 24 83 132 2.8 1 118 14 84 142 2.8 1 121 21 85 132 2.8 1 120 12 86 187 2.8 1 153 34 87 165 2.8 1 138 27 88 159 2.8 1 136 23 89 163 2.8 1 142 21 90 192 2.8 1 170 22 91 163 2.8 1 140 23 92 197 2.8 1 185 12 93 149 2.8 1 136 13 94 138 2.8 1 121 17 95 138 2.8 1 122 16 96 141 2.8 1 123 18 97 184 2.8 1 157 27 98 199 2.8 1 171 28 99 195 2.8 1 166 29 100 168 2.8 1 150 18 101 186 2.8 1 166 20 102 182 2.8 1 157 25 103 172 2.8 1 152 20 104 177 2.8 1 161 16 105 164 2.8 1 145 19 106 124 2.8 1 104 20 107 176 2.8 1 150 26 108 203 2.8 1 173 30 109 175 2.8 1 157 18 110 175 2.8 1 154 21 111 182 2.8 1 161 21 112 162 2.8 1 144 18 113 166 2.8 1 136 30 114 158 2.8 1 142 16 115 182 2.8 1 160 22 116 214 2.8 1 184 30 117 194 2.8 1 175 19 118 206 2.8 1 178 28 119 182 2.8 1 159 23 120 192 2.8 1 166 26 121 201 2.8 1 178 23 122 182 2.8 1 166 16 123 214 2.8 1 178 36 124 210 2.8 1 186 24 125 218 2.8 1 190 28 126 187 2.8 1 166 21 127 206 2.8 1 185 21 128 254 2.8 1 223 31 129 208 2.8 1 182 26 130 234 2.8 1 209 25 131 233 2.8 1 204 29 132 251 2.8 1 224 27 133 260 2.8 1 212 48 134 271 2.8 1 195 76 135 393 2.8 1 178 215 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R2.fq.gz ============================================= 190890981 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 190890981 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2320519 (1.22%)