SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308518_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: 66954). 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 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR12308518_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1823.605 s (20.094 µs/read; 2.99 M reads/minute). === Summary === Total reads processed: 90,755,093 Reads with adapters: 47,883,402 (52.8%) Reads written (passing filters): 90,755,093 (100.0%) Total basepairs processed: 13,704,019,043 bp Quality-trimmed: 76,196,166 bp (0.6%) Total written (filtered): 13,351,453,608 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 47883402 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.1% C: 18.9% G: 0.9% T: 30.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 38714561 22688773.2 0 38714561 2 513444 5672193.3 0 513444 3 348412 1418048.3 0 348412 4 260837 354512.1 0 260837 5 268721 88628.0 0 268721 6 234595 22157.0 0 234595 7 227917 5539.3 0 227917 8 274550 1384.8 0 274550 9 145534 346.2 0 145123 411 10 233385 86.6 1 205493 27892 11 208523 21.6 1 185941 22582 12 214550 5.4 1 173105 41445 13 207707 1.4 1 163997 43710 14 244487 1.4 1 190579 53908 15 166192 1.4 1 132837 33355 16 191662 1.4 1 151680 39982 17 242428 1.4 1 194799 47629 18 125856 1.4 1 99967 25889 19 233929 1.4 1 185103 48826 20 192102 1.4 1 153543 38559 21 103910 1.4 1 83231 20679 22 167067 1.4 1 133223 33844 23 164942 1.4 1 130899 34043 24 217403 1.4 1 172160 45243 25 189072 1.4 1 151451 37621 26 114242 1.4 1 91143 23099 27 99982 1.4 1 79737 20245 28 161658 1.4 1 131073 30585 29 117201 1.4 1 95107 22094 30 148579 1.4 1 119506 29073 31 115015 1.4 1 92767 22248 32 133688 1.4 1 107686 26002 33 114859 1.4 1 93008 21851 34 130157 1.4 1 106027 24130 35 102698 1.4 1 83975 18723 36 128385 1.4 1 103760 24625 37 113338 1.4 1 92475 20863 38 122677 1.4 1 101018 21659 39 101667 1.4 1 83300 18367 40 80835 1.4 1 66845 13990 41 78762 1.4 1 64907 13855 42 93305 1.4 1 76930 16375 43 83343 1.4 1 68375 14968 44 84123 1.4 1 69002 15121 45 89571 1.4 1 73560 16011 46 79387 1.4 1 65439 13948 47 73827 1.4 1 61537 12290 48 70077 1.4 1 58190 11887 49 71079 1.4 1 58919 12160 50 65372 1.4 1 54606 10766 51 62897 1.4 1 52425 10472 52 62074 1.4 1 51890 10184 53 58900 1.4 1 49580 9320 54 66310 1.4 1 55961 10349 55 44306 1.4 1 37196 7110 56 54213 1.4 1 45447 8766 57 68126 1.4 1 57546 10580 58 36103 1.4 1 30229 5874 59 40810 1.4 1 34673 6137 60 48724 1.4 1 41391 7333 61 45010 1.4 1 38331 6679 62 33407 1.4 1 28340 5067 63 66412 1.4 1 56946 9466 64 31152 1.4 1 26343 4809 65 23803 1.4 1 20301 3502 66 22455 1.4 1 19233 3222 67 35489 1.4 1 30649 4840 68 30755 1.4 1 26561 4194 69 25595 1.4 1 22227 3368 70 27849 1.4 1 24307 3542 71 25045 1.4 1 21854 3191 72 24867 1.4 1 21701 3166 73 31426 1.4 1 27533 3893 74 21689 1.4 1 18999 2690 75 21354 1.4 1 18944 2410 76 12389 1.4 1 10945 1444 77 11890 1.4 1 10415 1475 78 12578 1.4 1 10939 1639 79 12332 1.4 1 10898 1434 80 11761 1.4 1 10380 1381 81 11164 1.4 1 9915 1249 82 10510 1.4 1 9336 1174 83 10361 1.4 1 9209 1152 84 9627 1.4 1 8505 1122 85 9278 1.4 1 8210 1068 86 8221 1.4 1 7268 953 87 7634 1.4 1 6806 828 88 7009 1.4 1 6264 745 89 6721 1.4 1 6030 691 90 6035 1.4 1 5443 592 91 5709 1.4 1 5116 593 92 5265 1.4 1 4718 547 93 4863 1.4 1 4380 483 94 4369 1.4 1 3942 427 95 3935 1.4 1 3543 392 96 3572 1.4 1 3214 358 97 3458 1.4 1 3139 319 98 3267 1.4 1 2942 325 99 3237 1.4 1 2932 305 100 2750 1.4 1 2509 241 101 2455 1.4 1 2244 211 102 1933 1.4 1 1746 187 103 1830 1.4 1 1684 146 104 1562 1.4 1 1426 136 105 1500 1.4 1 1373 127 106 1300 1.4 1 1188 112 107 1125 1.4 1 1026 99 108 1062 1.4 1 989 73 109 904 1.4 1 822 82 110 758 1.4 1 692 66 111 683 1.4 1 631 52 112 603 1.4 1 549 54 113 512 1.4 1 470 42 114 442 1.4 1 394 48 115 411 1.4 1 369 42 116 309 1.4 1 276 33 117 282 1.4 1 256 26 118 224 1.4 1 188 36 119 262 1.4 1 216 46 120 254 1.4 1 226 28 121 228 1.4 1 194 34 122 218 1.4 1 191 27 123 181 1.4 1 160 21 124 160 1.4 1 144 16 125 148 1.4 1 132 16 126 141 1.4 1 122 19 127 145 1.4 1 134 11 128 121 1.4 1 100 21 129 130 1.4 1 114 16 130 98 1.4 1 87 11 131 112 1.4 1 96 16 132 73 1.4 1 66 7 133 85 1.4 1 73 12 134 77 1.4 1 74 3 135 79 1.4 1 71 8 136 61 1.4 1 58 3 137 54 1.4 1 45 9 138 53 1.4 1 44 9 139 65 1.4 1 59 6 140 48 1.4 1 40 8 141 46 1.4 1 40 6 142 33 1.4 1 28 5 143 26 1.4 1 23 3 144 42 1.4 1 34 8 145 43 1.4 1 36 7 146 36 1.4 1 27 9 147 43 1.4 1 27 16 148 36 1.4 1 25 11 149 28 1.4 1 21 7 150 25 1.4 1 17 8 151 37 1.4 1 18 19 RUN STATISTICS FOR INPUT FILE: ERR12308518_1.fastq.gz ============================================= 90755093 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 90755093 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36023 (0.04%)