SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245584_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 339695). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245584_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4687.195 s (44.676 µs/read; 1.34 M reads/minute). === Summary === Total reads processed: 104,914,304 Reads with adapters: 72,149,047 (68.8%) Reads written (passing filters): 104,914,304 (100.0%) Total basepairs processed: 15,737,145,600 bp Quality-trimmed: 92,368,859 bp (0.6%) Total written (filtered): 12,759,198,756 bp (81.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72149047 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.0% C: 17.0% G: 1.3% T: 36.0% none/other: 2.6% Overview of removed sequences length count expect max.err error counts 1 31485299 26228576.0 0 31485299 2 517052 6557144.0 0 517052 3 509759 1639286.0 0 509759 4 459285 409821.5 0 459285 5 455743 102455.4 0 455743 6 379722 25613.8 0 379722 7 395250 6403.5 0 395250 8 435813 1600.9 0 435813 9 331210 400.2 0 329608 1602 10 406371 100.1 1 371698 34673 11 405339 25.0 1 358218 47121 12 409536 6.3 1 367303 42233 13 378846 1.6 1 343536 35310 14 399352 1.6 1 359797 39555 15 360815 1.6 1 326448 34367 16 382329 1.6 1 342777 39552 17 408050 1.6 1 371728 36322 18 310853 1.6 1 282563 28290 19 390009 1.6 1 353976 36033 20 379232 1.6 1 345650 33582 21 314044 1.6 1 279708 34336 22 338555 1.6 1 309723 28832 23 328674 1.6 1 302347 26327 24 388325 1.6 1 353560 34765 25 384932 1.6 1 354681 30251 26 263175 1.6 1 237735 25440 27 291739 1.6 1 261187 30552 28 322096 1.6 1 298799 23297 29 306656 1.6 1 276080 30576 30 315029 1.6 1 289243 25786 31 288526 1.6 1 264353 24173 32 295167 1.6 1 273270 21897 33 336046 1.6 1 308654 27392 34 280627 1.6 1 249361 31266 35 283272 1.6 1 258699 24573 36 296793 1.6 1 276434 20359 37 271447 1.6 1 249482 21965 38 268819 1.6 1 247501 21318 39 293165 1.6 1 269851 23314 40 248782 1.6 1 228817 19965 41 263772 1.6 1 245301 18471 42 373892 1.6 1 351109 22783 43 185176 1.6 1 165582 19594 44 508575 1.6 1 482263 26312 45 341446 1.6 1 316530 24916 46 212848 1.6 1 185580 27268 47 502072 1.6 1 483720 18352 48 92257 1.6 1 78784 13473 49 253858 1.6 1 233861 19997 50 84017 1.6 1 76114 7903 51 156979 1.6 1 142898 14081 52 99313 1.6 1 89452 9861 53 217970 1.6 1 205064 12906 54 357667 1.6 1 342506 15161 55 104611 1.6 1 93399 11212 56 249106 1.6 1 226109 22997 57 980066 1.6 1 952255 27811 58 162025 1.6 1 146774 15251 59 83738 1.6 1 71722 12016 60 556699 1.6 1 537466 19233 61 99577 1.6 1 91912 7665 62 77324 1.6 1 66322 11002 63 486301 1.6 1 462488 23813 64 722188 1.6 1 704549 17639 65 79628 1.6 1 71209 8419 66 154870 1.6 1 145648 9222 67 87581 1.6 1 82651 4930 68 63549 1.6 1 56593 6956 69 99688 1.6 1 92744 6944 70 160260 1.6 1 152541 7719 71 70711 1.6 1 64926 5785 72 67336 1.6 1 61612 5724 73 91370 1.6 1 84178 7192 74 113915 1.6 1 104129 9786 75 192639 1.6 1 177082 15557 76 248513 1.6 1 231221 17292 77 185779 1.6 1 172291 13488 78 192225 1.6 1 181063 11162 79 195450 1.6 1 184678 10772 80 200345 1.6 1 189819 10526 81 206879 1.6 1 195850 11029 82 220256 1.6 1 206991 13265 83 267022 1.6 1 252734 14288 84 254067 1.6 1 238737 15330 85 288587 1.6 1 273628 14959 86 248972 1.6 1 235762 13210 87 224635 1.6 1 212268 12367 88 221022 1.6 1 209024 11998 89 210768 1.6 1 200640 10128 90 213003 1.6 1 203806 9197 91 208302 1.6 1 199465 8837 92 212075 1.6 1 203208 8867 93 214642 1.6 1 205722 8920 94 213527 1.6 1 204321 9206 95 216604 1.6 1 207346 9258 96 217591 1.6 1 208770 8821 97 223239 1.6 1 214189 9050 98 235615 1.6 1 226466 9149 99 247236 1.6 1 238111 9125 100 252553 1.6 1 243712 8841 101 236731 1.6 1 227921 8810 102 230143 1.6 1 221376 8767 103 227998 1.6 1 219239 8759 104 227810 1.6 1 219231 8579 105 235321 1.6 1 226826 8495 106 238380 1.6 1 229891 8489 107 244193 1.6 1 235597 8596 108 247838 1.6 1 239064 8774 109 243310 1.6 1 234501 8809 110 244459 1.6 1 235556 8903 111 246947 1.6 1 238011 8936 112 249181 1.6 1 240097 9084 113 258173 1.6 1 249043 9130 114 267170 1.6 1 257944 9226 115 266914 1.6 1 257436 9478 116 280416 1.6 1 270925 9491 117 275840 1.6 1 266106 9734 118 277725 1.6 1 267735 9990 119 278846 1.6 1 268575 10271 120 278420 1.6 1 267699 10721 121 275265 1.6 1 264603 10662 122 267970 1.6 1 257116 10854 123 280243 1.6 1 268234 12009 124 268318 1.6 1 256249 12069 125 269139 1.6 1 255982 13157 126 258131 1.6 1 244007 14124 127 245310 1.6 1 229215 16095 128 245175 1.6 1 224410 20765 129 248308 1.6 1 218001 30307 130 240358 1.6 1 197397 42961 131 253547 1.6 1 188509 65038 132 261993 1.6 1 174193 87800 133 268581 1.6 1 162095 106486 134 252831 1.6 1 142845 109986 135 237810 1.6 1 127041 110769 136 210609 1.6 1 108355 102254 137 180526 1.6 1 104464 76062 138 163978 1.6 1 110807 53171 139 145221 1.6 1 104904 40317 140 140915 1.6 1 108584 32331 141 158335 1.6 1 133047 25288 142 127536 1.6 1 110056 17480 143 129248 1.6 1 110682 18566 144 178706 1.6 1 151471 27235 145 228524 1.6 1 191250 37274 146 120542 1.6 1 96525 24017 147 19880 1.6 1 13902 5978 148 215118 1.6 1 177682 37436 149 91252 1.6 1 72624 18628 150 1822198 1.6 1 1544906 277292 RUN STATISTICS FOR INPUT FILE: SRR18245584_2.fastq.gz ============================================= 104914304 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 104914304 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5831632 (5.56%)