SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684007_1.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: 235230). 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 ERR10684007_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1429.668 s (18.546 µs/read; 3.24 M reads/minute). === Summary === Total reads processed: 77,086,148 Reads with adapters: 51,640,764 (67.0%) Reads written (passing filters): 77,086,148 (100.0%) Total basepairs processed: 11,640,008,348 bp Quality-trimmed: 42,705,062 bp (0.4%) Total written (filtered): 10,750,491,034 bp (92.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 51640764 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 53.0% C: 18.1% G: 0.9% T: 28.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25412496 19271537.0 0 25412496 2 1074402 4817884.2 0 1074402 3 682461 1204471.1 0 682461 4 574982 301117.8 0 574982 5 602285 75279.4 0 602285 6 595904 18819.9 0 595904 7 608642 4705.0 0 608642 8 726728 1176.2 0 726728 9 457115 294.1 0 455072 2043 10 609992 73.5 1 537120 72872 11 510646 18.4 1 456860 53786 12 536873 4.6 1 466855 70018 13 497136 1.1 1 432746 64390 14 593095 1.1 1 511737 81358 15 376192 1.1 1 331086 45106 16 487250 1.1 1 430372 56878 17 669905 1.1 1 589487 80418 18 347383 1.1 1 306027 41356 19 624648 1.1 1 547232 77416 20 476249 1.1 1 421441 54808 21 324456 1.1 1 289110 35346 22 410070 1.1 1 363762 46308 23 396856 1.1 1 350648 46208 24 464115 1.1 1 402430 61685 25 443848 1.1 1 394094 49754 26 341298 1.1 1 303456 37842 27 314853 1.1 1 278174 36679 28 474669 1.1 1 422301 52368 29 379144 1.1 1 339724 39420 30 506349 1.1 1 452452 53897 31 314808 1.1 1 281572 33236 32 381319 1.1 1 337603 43716 33 312401 1.1 1 279017 33384 34 330984 1.1 1 298091 32893 35 242384 1.1 1 218185 24199 36 362502 1.1 1 325959 36543 37 229059 1.1 1 205859 23200 38 347992 1.1 1 311939 36053 39 359066 1.1 1 326341 32725 40 256293 1.1 1 232514 23779 41 301573 1.1 1 272675 28898 42 292627 1.1 1 265070 27557 43 223626 1.1 1 203550 20076 44 232017 1.1 1 209624 22393 45 237455 1.1 1 214811 22644 46 231324 1.1 1 210380 20944 47 223126 1.1 1 202014 21112 48 228188 1.1 1 207612 20576 49 252621 1.1 1 230299 22322 50 235510 1.1 1 215313 20197 51 216886 1.1 1 198524 18362 52 207388 1.1 1 190184 17204 53 194997 1.1 1 177838 17159 54 212678 1.1 1 193794 18884 55 140398 1.1 1 128989 11409 56 174751 1.1 1 159705 15046 57 239511 1.1 1 218879 20632 58 126428 1.1 1 115146 11282 59 178691 1.1 1 165243 13448 60 213098 1.1 1 195862 17236 61 195191 1.1 1 180295 14896 62 154884 1.1 1 142906 11978 63 228213 1.1 1 210900 17313 64 113391 1.1 1 104081 9310 65 121827 1.1 1 113250 8577 66 92064 1.1 1 84947 7117 67 134428 1.1 1 124457 9971 68 134464 1.1 1 124441 10023 69 127709 1.1 1 118325 9384 70 139273 1.1 1 129521 9752 71 139173 1.1 1 129269 9904 72 134254 1.1 1 124805 9449 73 154432 1.1 1 143703 10729 74 125768 1.1 1 117304 8464 75 113225 1.1 1 106309 6916 76 70211 1.1 1 65626 4585 77 68213 1.1 1 63525 4688 78 72164 1.1 1 67274 4890 79 73431 1.1 1 68542 4889 80 77067 1.1 1 71878 5189 81 78214 1.1 1 73094 5120 82 72626 1.1 1 67933 4693 83 66801 1.1 1 62585 4216 84 62321 1.1 1 58465 3856 85 59199 1.1 1 55440 3759 86 54773 1.1 1 51364 3409 87 51868 1.1 1 48697 3171 88 48891 1.1 1 45926 2965 89 48317 1.1 1 45358 2959 90 49337 1.1 1 46562 2775 91 47061 1.1 1 44354 2707 92 44954 1.1 1 42420 2534 93 42976 1.1 1 40532 2444 94 36885 1.1 1 34713 2172 95 34210 1.1 1 32251 1959 96 31127 1.1 1 29407 1720 97 28734 1.1 1 27102 1632 98 27662 1.1 1 26086 1576 99 27288 1.1 1 25809 1479 100 25812 1.1 1 24460 1352 101 23768 1.1 1 22443 1325 102 21809 1.1 1 20669 1140 103 19651 1.1 1 18615 1036 104 17261 1.1 1 16352 909 105 15887 1.1 1 15116 771 106 13917 1.1 1 13170 747 107 12970 1.1 1 12375 595 108 11854 1.1 1 11260 594 109 10507 1.1 1 9952 555 110 9794 1.1 1 9313 481 111 8822 1.1 1 8410 412 112 7914 1.1 1 7545 369 113 6597 1.1 1 6291 306 114 5667 1.1 1 5395 272 115 4521 1.1 1 4316 205 116 3892 1.1 1 3723 169 117 3259 1.1 1 3123 136 118 2714 1.1 1 2589 125 119 2174 1.1 1 2093 81 120 3473 1.1 1 3307 166 121 1500 1.1 1 1439 61 122 1046 1.1 1 1002 44 123 785 1.1 1 749 36 124 551 1.1 1 511 40 125 314 1.1 1 293 21 126 299 1.1 1 283 16 127 179 1.1 1 159 20 128 135 1.1 1 119 16 129 142 1.1 1 127 15 130 86 1.1 1 77 9 131 57 1.1 1 52 5 132 47 1.1 1 34 13 133 71 1.1 1 58 13 134 59 1.1 1 46 13 135 56 1.1 1 46 10 136 43 1.1 1 29 14 137 45 1.1 1 36 9 138 28 1.1 1 23 5 139 45 1.1 1 38 7 140 40 1.1 1 27 13 141 41 1.1 1 29 12 142 21 1.1 1 10 11 143 24 1.1 1 13 11 144 27 1.1 1 18 9 145 43 1.1 1 34 9 146 26 1.1 1 11 15 147 39 1.1 1 25 14 148 36 1.1 1 19 17 149 46 1.1 1 30 16 150 21 1.1 1 9 12 151 280 1.1 1 199 81 RUN STATISTICS FOR INPUT FILE: ERR10684007_1.fastq.gz ============================================= 77086148 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 77086148 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 74890 (0.10%)