SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308524_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: 120220). 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 ERR12308524_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1533.209 s (17.382 µs/read; 3.45 M reads/minute). === Summary === Total reads processed: 88,207,556 Reads with adapters: 50,137,973 (56.8%) Reads written (passing filters): 88,207,556 (100.0%) Total basepairs processed: 13,319,340,956 bp Quality-trimmed: 75,876,396 bp (0.6%) Total written (filtered): 12,771,415,603 bp (95.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 50137973 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.1% C: 20.6% G: 1.5% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 34684412 22051889.0 0 34684412 2 701348 5512972.2 0 701348 3 512956 1378243.1 0 512956 4 397281 344560.8 0 397281 5 417336 86140.2 0 417336 6 371817 21535.0 0 371817 7 356562 5383.8 0 356562 8 443762 1345.9 0 443762 9 213899 336.5 0 213320 579 10 365014 84.1 1 322853 42161 11 319357 21.0 1 286664 32693 12 336611 5.3 1 279178 57433 13 333094 1.3 1 269691 63403 14 396959 1.3 1 316970 79989 15 269242 1.3 1 221353 47889 16 317713 1.3 1 259080 58633 17 413353 1.3 1 341076 72277 18 202789 1.3 1 165625 37164 19 397250 1.3 1 322661 74589 20 295976 1.3 1 243340 52636 21 164017 1.3 1 135250 28767 22 267555 1.3 1 218857 48698 23 265724 1.3 1 216972 48752 24 361573 1.3 1 292986 68587 25 315476 1.3 1 260120 55356 26 190426 1.3 1 155870 34556 27 169325 1.3 1 139636 29689 28 274293 1.3 1 228183 46110 29 205650 1.3 1 172501 33149 30 256061 1.3 1 211695 44366 31 185718 1.3 1 154492 31226 32 218967 1.3 1 181241 37726 33 189384 1.3 1 157713 31671 34 213380 1.3 1 177509 35871 35 194273 1.3 1 163633 30640 36 199657 1.3 1 167496 32161 37 193667 1.3 1 163271 30396 38 166106 1.3 1 139888 26218 39 177130 1.3 1 149950 27180 40 175631 1.3 1 147982 27649 41 159295 1.3 1 135629 23666 42 174922 1.3 1 148430 26492 43 135323 1.3 1 114580 20743 44 151317 1.3 1 127335 23982 45 158807 1.3 1 133676 25131 46 137217 1.3 1 116518 20699 47 142410 1.3 1 121557 20853 48 130412 1.3 1 111151 19261 49 131469 1.3 1 112612 18857 50 124951 1.3 1 107346 17605 51 117013 1.3 1 100786 16227 52 118377 1.3 1 101829 16548 53 110355 1.3 1 95227 15128 54 124556 1.3 1 107790 16766 55 88403 1.3 1 76895 11508 56 105302 1.3 1 90870 14432 57 130901 1.3 1 113348 17553 58 75346 1.3 1 65467 9879 59 84237 1.3 1 74177 10060 60 100546 1.3 1 88172 12374 61 91479 1.3 1 80130 11349 62 68210 1.3 1 59921 8289 63 134714 1.3 1 118595 16119 64 64908 1.3 1 56714 8194 65 49552 1.3 1 43560 5992 66 47694 1.3 1 42197 5497 67 76367 1.3 1 67975 8392 68 66075 1.3 1 58780 7295 69 55928 1.3 1 49771 6157 70 61432 1.3 1 54909 6523 71 55996 1.3 1 50098 5898 72 54297 1.3 1 48800 5497 73 69684 1.3 1 62953 6731 74 48785 1.3 1 44014 4771 75 48346 1.3 1 44207 4139 76 27590 1.3 1 25035 2555 77 26918 1.3 1 24265 2653 78 28563 1.3 1 25838 2725 79 27850 1.3 1 25308 2542 80 27326 1.3 1 24844 2482 81 26049 1.3 1 23564 2485 82 24499 1.3 1 22313 2186 83 24331 1.3 1 22142 2189 84 22654 1.3 1 20694 1960 85 21871 1.3 1 20016 1855 86 19829 1.3 1 18227 1602 87 17964 1.3 1 16590 1374 88 17023 1.3 1 15560 1463 89 16033 1.3 1 14697 1336 90 15523 1.3 1 14315 1208 91 14302 1.3 1 13187 1115 92 13511 1.3 1 12459 1052 93 12446 1.3 1 11525 921 94 11294 1.3 1 10452 842 95 10326 1.3 1 9534 792 96 9837 1.3 1 9132 705 97 8996 1.3 1 8294 702 98 8655 1.3 1 8048 607 99 8398 1.3 1 7743 655 100 7889 1.3 1 7366 523 101 6796 1.3 1 6330 466 102 6035 1.3 1 5598 437 103 5468 1.3 1 5102 366 104 4871 1.3 1 4553 318 105 4527 1.3 1 4237 290 106 4117 1.3 1 3881 236 107 3819 1.3 1 3538 281 108 3263 1.3 1 3048 215 109 2885 1.3 1 2693 192 110 2676 1.3 1 2505 171 111 2491 1.3 1 2346 145 112 2158 1.3 1 2020 138 113 1876 1.3 1 1757 119 114 1600 1.3 1 1486 114 115 1459 1.3 1 1361 98 116 1238 1.3 1 1151 87 117 1041 1.3 1 969 72 118 1024 1.3 1 955 69 119 752 1.3 1 685 67 120 970 1.3 1 876 94 121 714 1.3 1 642 72 122 476 1.3 1 425 51 123 350 1.3 1 296 54 124 328 1.3 1 283 45 125 234 1.3 1 199 35 126 223 1.3 1 176 47 127 197 1.3 1 152 45 128 153 1.3 1 118 35 129 113 1.3 1 89 24 130 115 1.3 1 87 28 131 92 1.3 1 70 22 132 74 1.3 1 60 14 133 77 1.3 1 62 15 134 51 1.3 1 41 10 135 73 1.3 1 57 16 136 56 1.3 1 49 7 137 47 1.3 1 35 12 138 41 1.3 1 28 13 139 40 1.3 1 31 9 140 41 1.3 1 29 12 141 31 1.3 1 21 10 142 24 1.3 1 14 10 143 34 1.3 1 18 16 144 26 1.3 1 10 16 145 32 1.3 1 23 9 146 23 1.3 1 9 14 147 28 1.3 1 11 17 148 35 1.3 1 16 19 149 25 1.3 1 14 11 150 25 1.3 1 11 14 151 82 1.3 1 20 62 RUN STATISTICS FOR INPUT FILE: ERR12308524_2.fastq.gz ============================================= 88207556 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88207556 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 29551 (0.03%)