SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10683999_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: 142975). Second best hit was smallRNA (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 ERR10683999_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1538.489 s (16.335 µs/read; 3.67 M reads/minute). === Summary === Total reads processed: 94,184,185 Reads with adapters: 55,845,744 (59.3%) Reads written (passing filters): 94,184,185 (100.0%) Total basepairs processed: 14,221,811,935 bp Quality-trimmed: 57,822,499 bp (0.4%) Total written (filtered): 13,471,633,119 bp (94.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55845744 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.7% C: 19.3% G: 0.8% T: 29.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37558726 23546046.2 0 37558726 2 646447 5886511.6 0 646447 3 436779 1471627.9 0 436779 4 322400 367907.0 0 322400 5 333973 91976.7 0 333973 6 319454 22994.2 0 319454 7 321291 5748.5 0 321291 8 377736 1437.1 0 377736 9 245850 359.3 0 245156 694 10 326942 89.8 1 295400 31542 11 294461 22.5 1 269821 24640 12 309415 5.6 1 267843 41572 13 309341 1.4 1 265773 43568 14 357658 1.4 1 305224 52434 15 249692 1.4 1 218004 31688 16 297046 1.4 1 259651 37395 17 398397 1.4 1 346818 51579 18 186073 1.4 1 161977 24096 19 377714 1.4 1 327687 50027 20 283366 1.4 1 247410 35956 21 193190 1.4 1 169935 23255 22 276708 1.4 1 242398 34310 23 277164 1.4 1 242490 34674 24 342725 1.4 1 295202 47523 25 315395 1.4 1 276700 38695 26 225733 1.4 1 198468 27265 27 202732 1.4 1 177419 25313 28 277795 1.4 1 244391 33404 29 235914 1.4 1 208804 27110 30 275442 1.4 1 242547 32895 31 226161 1.4 1 199937 26224 32 256716 1.4 1 225338 31378 33 222246 1.4 1 196692 25554 34 253504 1.4 1 222104 31400 35 269575 1.4 1 239725 29850 36 190864 1.4 1 169585 21279 37 224911 1.4 1 200274 24637 38 273865 1.4 1 244123 29742 39 195297 1.4 1 174106 21191 40 225776 1.4 1 202625 23151 41 185911 1.4 1 166412 19499 42 217420 1.4 1 195010 22410 43 195338 1.4 1 175594 19744 44 198975 1.4 1 178298 20677 45 208554 1.4 1 186591 21963 46 206405 1.4 1 185401 21004 47 181892 1.4 1 163057 18835 48 185675 1.4 1 166987 18688 49 189915 1.4 1 171324 18591 50 174982 1.4 1 157771 17211 51 166578 1.4 1 150906 15672 52 170237 1.4 1 154260 15977 53 169750 1.4 1 153332 16418 54 191521 1.4 1 172910 18611 55 135079 1.4 1 122477 12602 56 161441 1.4 1 145991 15450 57 206504 1.4 1 187091 19413 58 110025 1.4 1 99253 10772 59 138401 1.4 1 126378 12023 60 152159 1.4 1 138387 13772 61 145682 1.4 1 133259 12423 62 128256 1.4 1 117042 11214 63 206087 1.4 1 188899 17188 64 107913 1.4 1 97847 10066 65 118699 1.4 1 108885 9814 66 89567 1.4 1 81904 7663 67 125366 1.4 1 114974 10392 68 122662 1.4 1 112322 10340 69 107873 1.4 1 98902 8971 70 109133 1.4 1 100164 8969 71 106357 1.4 1 97707 8650 72 110832 1.4 1 101819 9013 73 141574 1.4 1 130582 10992 74 118720 1.4 1 109681 9039 75 110448 1.4 1 102380 8068 76 73969 1.4 1 68460 5509 77 67873 1.4 1 62550 5323 78 70787 1.4 1 65506 5281 79 69384 1.4 1 64172 5212 80 68477 1.4 1 63333 5144 81 66937 1.4 1 61953 4984 82 63727 1.4 1 59141 4586 83 64169 1.4 1 59538 4631 84 61296 1.4 1 56808 4488 85 60638 1.4 1 56348 4290 86 56662 1.4 1 52742 3920 87 53665 1.4 1 49957 3708 88 51219 1.4 1 47611 3608 89 50300 1.4 1 46839 3461 90 49112 1.4 1 46029 3083 91 44250 1.4 1 41286 2964 92 43219 1.4 1 40410 2809 93 41669 1.4 1 38996 2673 94 38261 1.4 1 35797 2464 95 36756 1.4 1 34344 2412 96 35147 1.4 1 32917 2230 97 32790 1.4 1 30717 2073 98 31859 1.4 1 29902 1957 99 30723 1.4 1 28813 1910 100 29147 1.4 1 27402 1745 101 25768 1.4 1 24247 1521 102 23492 1.4 1 22187 1305 103 21465 1.4 1 20177 1288 104 19252 1.4 1 18185 1067 105 18268 1.4 1 17201 1067 106 16756 1.4 1 15798 958 107 15424 1.4 1 14581 843 108 14088 1.4 1 13282 806 109 12056 1.4 1 11481 575 110 10760 1.4 1 10155 605 111 9837 1.4 1 9322 515 112 8581 1.4 1 8159 422 113 7642 1.4 1 7272 370 114 6677 1.4 1 6374 303 115 5726 1.4 1 5456 270 116 4799 1.4 1 4596 203 117 4014 1.4 1 3841 173 118 3405 1.4 1 3251 154 119 2844 1.4 1 2700 144 120 3488 1.4 1 3329 159 121 1890 1.4 1 1800 90 122 1379 1.4 1 1321 58 123 1031 1.4 1 963 68 124 826 1.4 1 780 46 125 618 1.4 1 585 33 126 506 1.4 1 470 36 127 338 1.4 1 313 25 128 251 1.4 1 230 21 129 259 1.4 1 241 18 130 182 1.4 1 172 10 131 184 1.4 1 165 19 132 110 1.4 1 95 15 133 160 1.4 1 142 18 134 89 1.4 1 72 17 135 105 1.4 1 90 15 136 92 1.4 1 79 13 137 96 1.4 1 82 14 138 58 1.4 1 46 12 139 78 1.4 1 61 17 140 41 1.4 1 32 9 141 76 1.4 1 64 12 142 43 1.4 1 25 18 143 36 1.4 1 27 9 144 45 1.4 1 28 17 145 38 1.4 1 30 8 146 40 1.4 1 19 21 147 46 1.4 1 30 16 148 45 1.4 1 24 21 149 62 1.4 1 43 19 150 36 1.4 1 15 21 151 201 1.4 1 138 63 RUN STATISTICS FOR INPUT FILE: ERR10683999_2.fastq.gz ============================================= 94184185 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 94184185 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 62527 (0.07%)