SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308514_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 143535). Second best hit was Nextera (count: 0) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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 Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR12308514_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1208.001 s (16.866 µs/read; 3.56 M reads/minute). === Summary === Total reads processed: 71,624,117 Reads with adapters: 39,253,338 (54.8%) Reads written (passing filters): 71,624,117 (100.0%) Total basepairs processed: 10,815,241,667 bp Quality-trimmed: 66,125,106 bp (0.6%) Total written (filtered): 10,290,754,348 bp (95.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39253338 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 21.6% G: 4.4% T: 27.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24239367 17906029.2 0 24239367 2 1048489 4476507.3 0 1048489 3 513258 1119126.8 0 513258 4 337938 279781.7 0 337938 5 351811 69945.4 0 351811 6 313358 17486.4 0 313358 7 303158 4371.6 0 303158 8 369134 1092.9 0 369134 9 188181 273.2 0 187321 860 10 315059 68.3 1 276499 38560 11 279544 17.1 1 247895 31649 12 298579 4.3 1 252143 46436 13 287396 1.1 1 241549 45847 14 339475 1.1 1 279999 59476 15 236493 1.1 1 200593 35900 16 273129 1.1 1 230698 42431 17 356313 1.1 1 303689 52624 18 178154 1.1 1 150085 28069 19 357200 1.1 1 299605 57595 20 276758 1.1 1 235960 40798 21 153930 1.1 1 130912 23018 22 254338 1.1 1 215051 39287 23 251450 1.1 1 212098 39352 24 347112 1.1 1 290050 57062 25 298038 1.1 1 254934 43104 26 172521 1.1 1 146186 26335 27 151216 1.1 1 128894 22322 28 260482 1.1 1 223883 36599 29 189920 1.1 1 164465 25455 30 255851 1.1 1 218459 37392 31 181981 1.1 1 156268 25713 32 238706 1.1 1 203596 35110 33 179301 1.1 1 154778 24523 34 219115 1.1 1 186989 32126 35 259818 1.1 1 226950 32868 36 203004 1.1 1 177298 25706 37 153555 1.1 1 133354 20201 38 137019 1.1 1 119319 17700 39 182424 1.1 1 159015 23409 40 204274 1.1 1 178205 26069 41 139461 1.1 1 122479 16982 42 175668 1.1 1 153685 21983 43 150026 1.1 1 131248 18778 44 157710 1.1 1 137061 20649 45 165171 1.1 1 143863 21308 46 145531 1.1 1 127450 18081 47 141655 1.1 1 124900 16755 48 132689 1.1 1 117029 15660 49 133385 1.1 1 117412 15973 50 126857 1.1 1 112564 14293 51 119776 1.1 1 106127 13649 52 122043 1.1 1 108063 13980 53 114784 1.1 1 102050 12734 54 125637 1.1 1 112003 13634 55 92162 1.1 1 82621 9541 56 107668 1.1 1 95632 12036 57 135234 1.1 1 120333 14901 58 72173 1.1 1 64460 7713 59 83609 1.1 1 75534 8075 60 99788 1.1 1 89378 10410 61 91938 1.1 1 82647 9291 62 69323 1.1 1 62523 6800 63 138393 1.1 1 125205 13188 64 65472 1.1 1 59032 6440 65 50196 1.1 1 45355 4841 66 48498 1.1 1 43748 4750 67 76217 1.1 1 69622 6595 68 66544 1.1 1 60655 5889 69 55735 1.1 1 50892 4843 70 60385 1.1 1 55488 4897 71 54890 1.1 1 50354 4536 72 54785 1.1 1 50285 4500 73 70461 1.1 1 65042 5419 74 49722 1.1 1 45931 3791 75 48137 1.1 1 44657 3480 76 28510 1.1 1 26269 2241 77 27794 1.1 1 25592 2202 78 29429 1.1 1 27105 2324 79 28878 1.1 1 26709 2169 80 28030 1.1 1 25826 2204 81 27197 1.1 1 25109 2088 82 26012 1.1 1 24083 1929 83 25321 1.1 1 23479 1842 84 24105 1.1 1 22321 1784 85 23151 1.1 1 21506 1645 86 20770 1.1 1 19282 1488 87 19494 1.1 1 18253 1241 88 18038 1.1 1 16803 1235 89 17425 1.1 1 16217 1208 90 16766 1.1 1 15668 1098 91 15015 1.1 1 13948 1067 92 14223 1.1 1 13292 931 93 13384 1.1 1 12509 875 94 11905 1.1 1 11121 784 95 11488 1.1 1 10777 711 96 10809 1.1 1 10113 696 97 10249 1.1 1 9610 639 98 9555 1.1 1 8988 567 99 9608 1.1 1 9041 567 100 8905 1.1 1 8380 525 101 7541 1.1 1 7075 466 102 6768 1.1 1 6303 465 103 6179 1.1 1 5790 389 104 5484 1.1 1 5136 348 105 5389 1.1 1 5076 313 106 4727 1.1 1 4424 303 107 4563 1.1 1 4275 288 108 4120 1.1 1 3880 240 109 3592 1.1 1 3385 207 110 3216 1.1 1 2995 221 111 2950 1.1 1 2747 203 112 2638 1.1 1 2485 153 113 2421 1.1 1 2290 131 114 1978 1.1 1 1848 130 115 1858 1.1 1 1748 110 116 1628 1.1 1 1541 87 117 1453 1.1 1 1341 112 118 1244 1.1 1 1133 111 119 1181 1.1 1 1084 97 120 2232 1.1 1 2128 104 121 1368 1.1 1 1273 95 122 689 1.1 1 627 62 123 641 1.1 1 576 65 124 523 1.1 1 459 64 125 490 1.1 1 423 67 126 383 1.1 1 311 72 127 320 1.1 1 268 52 128 296 1.1 1 251 45 129 264 1.1 1 217 47 130 225 1.1 1 182 43 131 203 1.1 1 173 30 132 159 1.1 1 130 29 133 172 1.1 1 142 30 134 120 1.1 1 92 28 135 136 1.1 1 103 33 136 140 1.1 1 106 34 137 127 1.1 1 107 20 138 93 1.1 1 72 21 139 86 1.1 1 70 16 140 76 1.1 1 53 23 141 97 1.1 1 75 22 142 81 1.1 1 60 21 143 74 1.1 1 43 31 144 66 1.1 1 34 32 145 73 1.1 1 50 23 146 78 1.1 1 49 29 147 77 1.1 1 38 39 148 67 1.1 1 41 26 149 77 1.1 1 47 30 150 35 1.1 1 17 18 151 307 1.1 1 73 234 RUN STATISTICS FOR INPUT FILE: ERR12308514_2.fastq.gz ============================================= 71624117 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 71624117 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 70004 (0.10%)