SUMMARISING RUN PARAMETERS ========================== Input filename: ERR13913462_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: 34166). 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 ERR13913462_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 2499.756 s (21.088 µs/read; 2.85 M reads/minute). === Summary === Total reads processed: 118,537,385 Reads with adapters: 62,515,779 (52.7%) Reads written (passing filters): 118,537,385 (100.0%) Total basepairs processed: 17,780,607,750 bp Quality-trimmed: 68,950,881 bp (0.4%) Total written (filtered): 17,503,876,633 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62515779 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.5% C: 17.5% G: 0.4% T: 29.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 56777803 29634346.2 0 56777803 2 205886 7408586.6 0 205886 3 196529 1852146.6 0 196529 4 170325 463036.7 0 170325 5 167412 115759.2 0 167412 6 138732 28939.8 0 138732 7 150531 7234.9 0 150531 8 162069 1808.7 0 162069 9 124908 452.2 0 124858 50 10 150688 113.0 1 140251 10437 11 143266 28.3 1 131270 11996 12 131283 7.1 1 92267 39016 13 119739 1.8 1 82767 36972 14 125132 1.8 1 87453 37679 15 106807 1.8 1 74559 32248 16 114755 1.8 1 79942 34813 17 142562 1.8 1 99919 42643 18 93961 1.8 1 65957 28004 19 142327 1.8 1 101537 40790 20 103909 1.8 1 72536 31373 21 90180 1.8 1 63769 26411 22 98609 1.8 1 70000 28609 23 94947 1.8 1 67670 27277 24 117416 1.8 1 84543 32873 25 113260 1.8 1 80326 32934 26 74460 1.8 1 53479 20981 27 79236 1.8 1 56492 22744 28 104520 1.8 1 76509 28011 29 92278 1.8 1 66516 25762 30 116329 1.8 1 85434 30895 31 92955 1.8 1 67766 25189 32 98422 1.8 1 72547 25875 33 93632 1.8 1 69107 24525 34 79833 1.8 1 59052 20781 35 81885 1.8 1 60010 21875 36 54159 1.8 1 40222 13937 37 65586 1.8 1 48598 16988 38 79361 1.8 1 59827 19534 39 61337 1.8 1 45492 15845 40 83784 1.8 1 63583 20201 41 62414 1.8 1 46190 16224 42 55953 1.8 1 42101 13852 43 55556 1.8 1 42042 13514 44 55851 1.8 1 42533 13318 45 48580 1.8 1 36812 11768 46 50761 1.8 1 38701 12060 47 50776 1.8 1 38510 12266 48 51542 1.8 1 39323 12219 49 47741 1.8 1 37017 10724 50 47689 1.8 1 36289 11400 51 51571 1.8 1 39438 12133 52 45371 1.8 1 35260 10111 53 40922 1.8 1 31600 9322 54 37586 1.8 1 28963 8623 55 33400 1.8 1 26294 7106 56 36119 1.8 1 28484 7635 57 28822 1.8 1 22399 6423 58 31282 1.8 1 24516 6766 59 41582 1.8 1 32971 8611 60 26300 1.8 1 20406 5894 61 32017 1.8 1 25412 6605 62 31964 1.8 1 25552 6412 63 23818 1.8 1 18748 5070 64 21157 1.8 1 16762 4395 65 35975 1.8 1 28856 7119 66 14399 1.8 1 11159 3240 67 13231 1.8 1 10335 2896 68 13705 1.8 1 11006 2699 69 18238 1.8 1 14679 3559 70 17998 1.8 1 14295 3703 71 14727 1.8 1 11965 2762 72 15922 1.8 1 12947 2975 73 13912 1.8 1 11207 2705 74 11777 1.8 1 9491 2286 75 16538 1.8 1 13421 3117 76 9714 1.8 1 7877 1837 77 6470 1.8 1 5160 1310 78 2840 1.8 1 2242 598 79 4500 1.8 1 3664 836 80 5601 1.8 1 4589 1012 81 5664 1.8 1 4667 997 82 5095 1.8 1 4210 885 83 4623 1.8 1 3781 842 84 3819 1.8 1 3105 714 85 3424 1.8 1 2818 606 86 2969 1.8 1 2356 613 87 2597 1.8 1 2085 512 88 2173 1.8 1 1720 453 89 2039 1.8 1 1633 406 90 1755 1.8 1 1369 386 91 1641 1.8 1 1268 373 92 1440 1.8 1 1097 343 93 1253 1.8 1 935 318 94 1064 1.8 1 788 276 95 936 1.8 1 664 272 96 718 1.8 1 526 192 97 722 1.8 1 503 219 98 619 1.8 1 421 198 99 565 1.8 1 361 204 100 505 1.8 1 327 178 101 456 1.8 1 302 154 102 415 1.8 1 264 151 103 362 1.8 1 226 136 104 371 1.8 1 220 151 105 280 1.8 1 149 131 106 299 1.8 1 162 137 107 293 1.8 1 153 140 108 261 1.8 1 136 125 109 271 1.8 1 142 129 110 252 1.8 1 137 115 111 209 1.8 1 115 94 112 220 1.8 1 120 100 113 209 1.8 1 126 83 114 174 1.8 1 99 75 115 182 1.8 1 106 76 116 167 1.8 1 102 65 117 156 1.8 1 94 62 118 198 1.8 1 108 90 119 158 1.8 1 89 69 120 175 1.8 1 101 74 121 153 1.8 1 92 61 122 152 1.8 1 97 55 123 150 1.8 1 104 46 124 134 1.8 1 81 53 125 149 1.8 1 92 57 126 129 1.8 1 86 43 127 108 1.8 1 63 45 128 99 1.8 1 66 33 129 101 1.8 1 66 35 130 92 1.8 1 65 27 131 91 1.8 1 51 40 132 69 1.8 1 52 17 133 55 1.8 1 31 24 134 60 1.8 1 50 10 135 44 1.8 1 29 15 136 37 1.8 1 24 13 137 36 1.8 1 29 7 138 35 1.8 1 23 12 139 30 1.8 1 25 5 140 23 1.8 1 14 9 141 12 1.8 1 10 2 142 21 1.8 1 13 8 143 13 1.8 1 9 4 144 14 1.8 1 7 7 145 21 1.8 1 13 8 146 21 1.8 1 15 6 147 16 1.8 1 8 8 148 20 1.8 1 8 12 149 17 1.8 1 8 9 150 14 1.8 1 5 9 RUN STATISTICS FOR INPUT FILE: ERR13913462_2.fastq.gz ============================================= 118537385 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 118537385 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19229 (0.02%)