SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684019_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: 83127). 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 ERR10684019_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1899.020 s (18.198 µs/read; 3.30 M reads/minute). === Summary === Total reads processed: 104,352,237 Reads with adapters: 58,216,635 (55.8%) Reads written (passing filters): 104,352,237 (100.0%) Total basepairs processed: 15,757,187,787 bp Quality-trimmed: 63,075,678 bp (0.4%) Total written (filtered): 15,251,031,847 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58216635 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.1% C: 17.6% G: 0.7% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 46413677 26088059.2 0 46413677 2 469814 6522014.8 0 469814 3 308713 1630503.7 0 308713 4 245400 407625.9 0 245400 5 251367 101906.5 0 251367 6 222757 25476.6 0 222757 7 214996 6369.2 0 214996 8 274170 1592.3 0 274170 9 164791 398.1 0 163998 793 10 236389 99.5 1 215997 20392 11 197184 24.9 1 176983 20201 12 230878 6.2 1 199024 31854 13 213454 1.6 1 185014 28440 14 258616 1.6 1 224076 34540 15 170905 1.6 1 147470 23435 16 201987 1.6 1 174751 27236 17 274388 1.6 1 240094 34294 18 123791 1.6 1 106577 17214 19 269473 1.6 1 234878 34595 20 199338 1.6 1 174932 24406 21 117483 1.6 1 101786 15697 22 187745 1.6 1 164060 23685 23 187916 1.6 1 163988 23928 24 234674 1.6 1 205025 29649 25 208757 1.6 1 184145 24612 26 167445 1.6 1 146619 20826 27 125555 1.6 1 108973 16582 28 208151 1.6 1 185524 22627 29 127037 1.6 1 110929 16108 30 218066 1.6 1 194358 23708 31 111309 1.6 1 97297 14012 32 229254 1.6 1 204328 24926 33 180647 1.6 1 161119 19528 34 117176 1.6 1 104901 12275 35 91658 1.6 1 80414 11244 36 215861 1.6 1 194339 21522 37 76777 1.6 1 67255 9522 38 197443 1.6 1 177914 19529 39 128625 1.6 1 114728 13897 40 89828 1.6 1 79703 10125 41 137971 1.6 1 123677 14294 42 150605 1.6 1 135206 15399 43 106142 1.6 1 94804 11338 44 122797 1.6 1 110795 12002 45 137355 1.6 1 123097 14258 46 123280 1.6 1 111171 12109 47 119399 1.6 1 108679 10720 48 97481 1.6 1 87869 9612 49 118154 1.6 1 106185 11969 50 101144 1.6 1 92538 8606 51 99399 1.6 1 90164 9235 52 100572 1.6 1 91368 9204 53 99564 1.6 1 90447 9117 54 119625 1.6 1 109337 10288 55 72486 1.6 1 65776 6710 56 95703 1.6 1 87052 8651 57 124817 1.6 1 114027 10790 58 71651 1.6 1 65070 6581 59 68410 1.6 1 62507 5903 60 103570 1.6 1 94886 8684 61 83372 1.6 1 76445 6927 62 58830 1.6 1 53662 5168 63 155440 1.6 1 144254 11186 64 58968 1.6 1 53861 5107 65 47072 1.6 1 43166 3906 66 46317 1.6 1 42519 3798 67 77037 1.6 1 71571 5466 68 65687 1.6 1 60497 5190 69 59943 1.6 1 55446 4497 70 68591 1.6 1 63741 4850 71 63949 1.6 1 59313 4636 72 61957 1.6 1 57203 4754 73 81329 1.6 1 75614 5715 74 50232 1.6 1 46684 3548 75 49053 1.6 1 45836 3217 76 36633 1.6 1 34067 2566 77 35282 1.6 1 32736 2546 78 37234 1.6 1 34674 2560 79 37025 1.6 1 34522 2503 80 36608 1.6 1 34156 2452 81 35828 1.6 1 33452 2376 82 35356 1.6 1 32946 2410 83 36128 1.6 1 33732 2396 84 33575 1.6 1 31434 2141 85 33366 1.6 1 31226 2140 86 31261 1.6 1 29250 2011 87 29508 1.6 1 27676 1832 88 27951 1.6 1 26221 1730 89 26914 1.6 1 25249 1665 90 26357 1.6 1 24783 1574 91 24502 1.6 1 23087 1415 92 23699 1.6 1 22332 1367 93 22848 1.6 1 21540 1308 94 21049 1.6 1 19879 1170 95 20365 1.6 1 19165 1200 96 19549 1.6 1 18430 1119 97 18210 1.6 1 17266 944 98 18548 1.6 1 17551 997 99 17771 1.6 1 16769 1002 100 16612 1.6 1 15744 868 101 14671 1.6 1 13915 756 102 13549 1.6 1 12870 679 103 12432 1.6 1 11788 644 104 11150 1.6 1 10581 569 105 10813 1.6 1 10268 545 106 9932 1.6 1 9429 503 107 9215 1.6 1 8793 422 108 8438 1.6 1 8064 374 109 7501 1.6 1 7114 387 110 6605 1.6 1 6276 329 111 6054 1.6 1 5760 294 112 5671 1.6 1 5397 274 113 4995 1.6 1 4786 209 114 4383 1.6 1 4211 172 115 3497 1.6 1 3333 164 116 2968 1.6 1 2841 127 117 2585 1.6 1 2478 107 118 2164 1.6 1 2079 85 119 1873 1.6 1 1800 73 120 7369 1.6 1 7070 299 121 1697 1.6 1 1621 76 122 915 1.6 1 881 34 123 731 1.6 1 697 34 124 511 1.6 1 477 34 125 411 1.6 1 380 31 126 340 1.6 1 322 18 127 277 1.6 1 254 23 128 215 1.6 1 198 17 129 181 1.6 1 169 12 130 158 1.6 1 147 11 131 161 1.6 1 142 19 132 106 1.6 1 97 9 133 128 1.6 1 108 20 134 99 1.6 1 85 14 135 118 1.6 1 104 14 136 87 1.6 1 81 6 137 111 1.6 1 96 15 138 70 1.6 1 61 9 139 86 1.6 1 70 16 140 72 1.6 1 60 12 141 83 1.6 1 69 14 142 60 1.6 1 42 18 143 60 1.6 1 38 22 144 41 1.6 1 30 11 145 63 1.6 1 50 13 146 55 1.6 1 34 21 147 58 1.6 1 38 20 148 35 1.6 1 26 9 149 59 1.6 1 36 23 150 35 1.6 1 25 10 151 171 1.6 1 132 39 RUN STATISTICS FOR INPUT FILE: ERR10684019_2.fastq.gz ============================================= 104352237 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 104352237 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 80082 (0.08%)