SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308523_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: 143366). 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 ERR12308523_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1410.888 s (21.472 µs/read; 2.79 M reads/minute). === Summary === Total reads processed: 65,707,566 Reads with adapters: 37,866,748 (57.6%) Reads written (passing filters): 65,707,566 (100.0%) Total basepairs processed: 9,921,842,466 bp Quality-trimmed: 53,366,856 bp (0.5%) Total written (filtered): 9,417,861,106 bp (94.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 37866748 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.7% C: 19.1% G: 1.4% T: 29.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24993520 16426891.5 0 24993520 2 503571 4106722.9 0 503571 3 338804 1026680.7 0 338804 4 263278 256670.2 0 263278 5 277362 64167.5 0 277362 6 246077 16041.9 0 246077 7 230550 4010.5 0 230550 8 299000 1002.6 0 299000 9 155966 250.7 0 155069 897 10 254201 62.7 1 221314 32887 11 218510 15.7 1 191993 26517 12 242444 3.9 1 203240 39204 13 233600 1.0 1 196461 37139 14 272128 1.0 1 224678 47450 15 195329 1.0 1 165050 30279 16 223728 1.0 1 188737 34991 17 290237 1.0 1 247835 42402 18 141644 1.0 1 118820 22824 19 288777 1.0 1 242244 46533 20 220750 1.0 1 188075 32675 21 124904 1.0 1 106061 18843 22 206105 1.0 1 174340 31765 23 204205 1.0 1 171950 32255 24 264294 1.0 1 221105 43189 25 236824 1.0 1 202438 34386 26 159361 1.0 1 134644 24717 27 142731 1.0 1 121084 21647 28 212482 1.0 1 183001 29481 29 160950 1.0 1 139178 21772 30 200552 1.0 1 171167 29385 31 161410 1.0 1 138617 22793 32 190631 1.0 1 163070 27561 33 167974 1.0 1 144308 23666 34 203480 1.0 1 175847 27633 35 135153 1.0 1 117521 17632 36 173943 1.0 1 151022 22921 37 156296 1.0 1 136758 19538 38 201227 1.0 1 174202 27025 39 133737 1.0 1 116604 17133 40 157025 1.0 1 138438 18587 41 131280 1.0 1 114785 16495 42 160508 1.0 1 140859 19649 43 133245 1.0 1 116266 16979 44 144330 1.0 1 125883 18447 45 154059 1.0 1 133792 20267 46 136498 1.0 1 119556 16942 47 134335 1.0 1 118703 15632 48 123836 1.0 1 109128 14708 49 130243 1.0 1 114335 15908 50 122550 1.0 1 109166 13384 51 118108 1.0 1 104727 13381 52 120181 1.0 1 106504 13677 53 116235 1.0 1 103484 12751 54 131686 1.0 1 117497 14189 55 89954 1.0 1 80473 9481 56 111813 1.0 1 99224 12589 57 145705 1.0 1 129867 15838 58 75788 1.0 1 67164 8624 59 85758 1.0 1 77380 8378 60 109876 1.0 1 98614 11262 61 98540 1.0 1 88876 9664 62 75463 1.0 1 67705 7758 63 158654 1.0 1 143388 15266 64 73005 1.0 1 65660 7345 65 57023 1.0 1 51489 5534 66 56039 1.0 1 50377 5662 67 88973 1.0 1 81272 7701 68 77169 1.0 1 70220 6949 69 66109 1.0 1 60212 5897 70 74440 1.0 1 68155 6285 71 67016 1.0 1 61437 5579 72 66447 1.0 1 60670 5777 73 87689 1.0 1 80669 7020 74 63288 1.0 1 58185 5103 75 63815 1.0 1 58968 4847 76 37676 1.0 1 34578 3098 77 35222 1.0 1 32238 2984 78 38093 1.0 1 35124 2969 79 37112 1.0 1 34180 2932 80 36783 1.0 1 33998 2785 81 35257 1.0 1 32424 2833 82 34214 1.0 1 31565 2649 83 33692 1.0 1 31120 2572 84 31746 1.0 1 29393 2353 85 31750 1.0 1 29324 2426 86 28765 1.0 1 26709 2056 87 26173 1.0 1 24405 1768 88 25089 1.0 1 23377 1712 89 23663 1.0 1 22017 1646 90 22393 1.0 1 20853 1540 91 21066 1.0 1 19627 1439 92 19855 1.0 1 18573 1282 93 18698 1.0 1 17437 1261 94 16554 1.0 1 15491 1063 95 16256 1.0 1 15189 1067 96 15020 1.0 1 14061 959 97 13876 1.0 1 12951 925 98 13529 1.0 1 12749 780 99 12896 1.0 1 12108 788 100 11956 1.0 1 11276 680 101 10406 1.0 1 9798 608 102 9152 1.0 1 8636 516 103 8507 1.0 1 8000 507 104 7706 1.0 1 7284 422 105 7231 1.0 1 6823 408 106 6422 1.0 1 6049 373 107 6148 1.0 1 5799 349 108 5290 1.0 1 5018 272 109 4630 1.0 1 4396 234 110 4180 1.0 1 3965 215 111 3920 1.0 1 3726 194 112 3379 1.0 1 3196 183 113 2883 1.0 1 2743 140 114 2467 1.0 1 2387 80 115 2096 1.0 1 1992 104 116 1679 1.0 1 1608 71 117 1593 1.0 1 1520 73 118 1279 1.0 1 1220 59 119 1076 1.0 1 1023 53 120 1267 1.0 1 1205 62 121 894 1.0 1 854 40 122 660 1.0 1 620 40 123 511 1.0 1 469 42 124 467 1.0 1 426 41 125 333 1.0 1 299 34 126 307 1.0 1 290 17 127 221 1.0 1 206 15 128 188 1.0 1 172 16 129 184 1.0 1 170 14 130 143 1.0 1 131 12 131 149 1.0 1 134 15 132 116 1.0 1 99 17 133 107 1.0 1 90 17 134 84 1.0 1 72 12 135 96 1.0 1 83 13 136 70 1.0 1 60 10 137 93 1.0 1 84 9 138 74 1.0 1 66 8 139 101 1.0 1 92 9 140 52 1.0 1 46 6 141 90 1.0 1 68 22 142 40 1.0 1 31 9 143 54 1.0 1 40 14 144 54 1.0 1 36 18 145 75 1.0 1 56 19 146 57 1.0 1 38 19 147 53 1.0 1 37 16 148 68 1.0 1 47 21 149 67 1.0 1 56 11 150 38 1.0 1 21 17 151 239 1.0 1 58 181 RUN STATISTICS FOR INPUT FILE: ERR12308523_1.fastq.gz ============================================= 65707566 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 65707566 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 48285 (0.07%)